VCV001560845.11 - ClinVar

NM_144643.4(SCLT1):c.638C>T (p.Thr213Ile)

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.

(5)

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.

Conflicting classifications of pathogenicity
Uncertain significance(3); Likely benign(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_144643.4(SCLT1):c.638C>T (p.Thr213Ile)

Variation ID: 1560845 Accession: VCV001560845.11

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 4q28.2 4: 128992215 (GRCh38) [ NCBI UCSC ] 4: 129913370 (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	Apr 8, 2022	Oct 8, 2024	Jan 21, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_144643.4:c.638C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_653244.2:p.Thr213Ile	missense
NM_144643.3:c.638C>T
NC_000004.12:g.128992215G>A
NC_000004.11:g.129913370G>A
NG_034202.1:g.106393C>T

... more HGVS ... less HGVS

Protein change

T213I

Other names

Canonical SPDI

NC_000004.12:128992214:G:A

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

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.

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

The Genome Aggregation Database (gnomAD) 0.00003

Trans-Omics for Precision Medicine (TOPMed) 0.00025

The Genome Aggregation Database (gnomAD), exomes 0.00028

Exome Aggregation Consortium (ExAC) 0.00031

Links

dbSNP: rs760824351 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.
SCLT1		-	-	GRCh38 GRCh37	475	510

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.
SCLT1-related disorder	Uncertain significance (2)	criteria provided, single submitter	Feb 1, 2022	RCV002243512.4
Tracheoesophageal fistula	Uncertain significance (1)	criteria provided, single submitter	Aug 22, 2022	RCV002279776.2
not provided	Conflicting interpretations of pathogenicity (2)	criteria provided, conflicting classifications	Jan 21, 2024	RCV002198064.8

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.
Uncertain significance (Aug 22, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Tracheoesophageal fistula Affected status: unknown Allele origin: maternal	Daryl Scott Lab, Baylor College of Medicine Accession: SCV002567951.1 First in ClinVar: Aug 29, 2022 Last updated: Aug 29, 2022	Publications: PubMed (1) PubMed: 36135330 Number of individuals with the variant: 1
Uncertain significance (Feb 01, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	SCLT1-related disorder Affected status: unknown Allele origin: biparental	Daryl Scott Lab, Baylor College of Medicine Accession: SCV002515376.1 First in ClinVar: May 21, 2022 Last updated: May 21, 2022	Publications: PubMed (1) PubMed: 36474027 Number of individuals with the variant: 1
Uncertain significance (Oct 12, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV004237143.1 First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024
Likely benign (Jan 21, 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: SCV002360355.3 First in ClinVar: Apr 08, 2022 Last updated: Feb 14, 2024
Likely benign (Jul 16, 2024)	no assertion criteria provided Method: clinical testing	SCLT1-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004782198.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
High molecular diagnostic yields and novel phenotypic expansions involving syndromic anorectal malformations.	Belanger Deloge R	European journal of human genetics : EJHG	2023	PMID: 36474027
Exome sequencing efficacy and phenotypic expansions involving esophageal atresia/tracheoesophageal fistula plus.	Sy MR	American journal of medical genetics. Part A	2022	PMID: 36135330

Text-mined citations for rs760824351 ...

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 Nov 19, 2024

ClinVar Genomic variation as it relates to human health

NM_144643.4(SCLT1):c.638C>T (p.Thr213Ile)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs760824351 ...