VCV000377350.50 - ClinVar

NM_015158.5(KANK1):c.149A>T (p.Asp50Val)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(7)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_015158.5(KANK1):c.149A>T (p.Asp50Val)

Variation ID: 377350 Accession: VCV000377350.50

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9p24.3 9: 710915 (GRCh38) [ NCBI UCSC ] 9: 710915 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 8, 2017	Oct 20, 2024	Jul 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_015158.5:c.149A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055973.2:p.Asp50Val	missense
NM_001256876.3:c.149A>T	NP_001243805.1:p.Asp50Val	missense
NM_001256877.3:c.149A>T	NP_001243806.1:p.Asp50Val	missense
NM_001354331.2:c.149A>T	NP_001341260.1:p.Asp50Val	missense
NM_001354332.2:c.149A>T	NP_001341261.1:p.Asp50Val	missense
NM_001354333.2:c.-326A>T		5 prime UTR
NM_001354334.2:c.149A>T	NP_001341263.1:p.Asp50Val	missense
NM_001354335.2:c.-326A>T		5 prime UTR
NM_001354336.2:c.-326A>T		5 prime UTR
NM_001354337.2:c.-326A>T		5 prime UTR
NM_001354338.2:c.-326A>T		5 prime UTR
NM_001354339.2:c.-326A>T		5 prime UTR
NM_001354340.2:c.-326A>T		5 prime UTR
NM_001354341.2:c.-326A>T		5 prime UTR
NM_001354342.2:c.-326A>T		5 prime UTR
NM_001354343.2:c.-326A>T		5 prime UTR
NM_001354344.2:c.-326A>T		5 prime UTR
NM_153186.6:c.-326A>T		5 prime UTR
NR_148869.2:n.311A>T		non-coding transcript variant
NC_000009.12:g.710915A>T
NC_000009.11:g.710915A>T
NG_016331.2:g.245622A>T

... more HGVS ... less HGVS

Protein change

D50V

Other names

Canonical SPDI

NC_000009.12:710914:A:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

unknown functional consequence

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00200 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 30x 0.00172

1000 Genomes Project 0.00200

The Genome Aggregation Database (gnomAD) 0.00617

Trans-Omics for Precision Medicine (TOPMed) 0.00699

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00746

Links

ClinGen: CA4959857 dbSNP: rs61737971 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
KANK1		No evidence available	No evidence available	GRCh38 GRCh37	821	1164

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Benign/Likely benign (5)	criteria provided, multiple submitters, no conflicts	Jul 1, 2024	RCV000430887.20
not specified	Likely benign (1)	criteria provided, single submitter	May 30, 2017	RCV000598207.4
Amyotrophic lateral sclerosis	Uncertain significance (1)	no assertion criteria provided	-	RCV003105894.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely Benign (Dec 28, 2016)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: not provided Allele origin: germline	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics Accession: SCV000511801.1 First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017	Comment: Converted during submission to Likely benign.
Likely benign (May 30, 2017)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000708962.2 First in ClinVar: Apr 02, 2018 Last updated: Apr 02, 2018	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KANK1 Number of individuals with the variant: 1 Sex: mixed
Benign (Mar 12, 2021)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001909497.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021
Likely benign (Jan 29, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001027052.4 First in ClinVar: Dec 17, 2019 Last updated: Feb 14, 2024
Likely benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Unknown mechanism) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005223041.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Likely benign (Jul 01, 2024)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004161734.10 First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024	Comment: KANK1: BS2 Number of individuals with the variant: 7
Uncertain significance (-)	no assertion criteria provided Method: research	Amyotrophic lateral sclerosis (Sporadic) Affected status: yes Allele origin: unknown	UM ALS/MND Lab, University Of Malta Accession: SCV002555579.2 First in ClinVar: Feb 13, 2023 Last updated: May 20, 2023	Age: 70-79 years Sex: male Ethnicity/Population group: Caucasian Geographic origin: Malta

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
unknown functional consequence	Method not provided	Result not provided	UM ALS/MND Lab, University Of Malta Accession: SCV002555579.2

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KANK1	-	-	-	-

Text-mined citations for rs61737971 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_015158.5(KANK1):c.149A>T (p.Asp50Val)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs61737971 ...