NM_001017995.3(SH3PXD2B):c.*3114A>G AND Frank-Ter Haar syndrome

Germline classification:: Benign (1 submission)
Last evaluated:: Apr 27, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001151185.4

Allele description [Variation Report for NM_001017995.3(SH3PXD2B):c.*3114A>G]

NM_001017995.3(SH3PXD2B):c.*3114A>G

Gene:

SH3PXD2B:SH3 and PX domains 2B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.1

Genomic location:

Preferred name:

NM_001017995.3(SH3PXD2B):c.*3114A>G

HGVS:

NC_000005.10:g.172335255T>C
NG_027746.2:g.124269A>G
NM_001017995.3:c.*3114A>GMANE SELECT
NM_001308175.2:c.1189-9875A>G
NC_000005.9:g.171762259T>C
NM_001017995.2:c.*3114A>G

Links:

dbSNP: rs147455605

NCBI 1000 Genomes Browser:

rs147455605

Molecular consequence:

NM_001017995.3:c.*3114A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001308175.2:c.1189-9875A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Frank-Ter Haar syndrome
Synonyms:: MELNICK-NEEDLES SYNDROME, AUTOSOMAL RECESSIVE; Ter Haar syndrome; Autosomal recessive Melnick-Needles syndrome (formerly); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009579; MedGen: C1855305; Orphanet: 1266; Orphanet: 137834; OMIM: 249420

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001312292	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001312292

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001312292.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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