NM_206933.4(USH2A):c.2109T>C (p.Asp703=) AND Usher syndrome, type 2A

Clinical significance:Benign/Likely benign (Last evaluated: Jul 1, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV001097278.3

Allele description [Variation Report for NM_206933.4(USH2A):c.2109T>C (p.Asp703=)]

NM_206933.4(USH2A):c.2109T>C (p.Asp703=)

Gene:
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.4(USH2A):c.2109T>C (p.Asp703=)
Other names:
p.D703D:GAT>GAC
HGVS:
  • NC_000001.11:g.216250961A>G
  • NG_009497.1:g.177436T>C
  • NG_009497.2:g.177488T>C
  • NM_007123.6:c.2109T>C
  • NM_206933.4:c.2109T>CMANE SELECT
  • NP_009054.6:p.Asp703=
  • NP_996816.3:p.Asp703=
  • NC_000001.10:g.216424303A>G
  • NM_007123.5:c.2109T>C
  • NM_206933.2:c.2109T>C
  • NM_206933.3:c.2109T>C
  • c.2109T>C
  • p.Asp703Asp
Links:
dbSNP: rs45555435
NCBI 1000 Genomes Browser:
rs45555435
Molecular consequence:
  • NM_007123.6:c.2109T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_206933.4:c.2109T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Usher syndrome, type 2A (USH2A)
Synonyms:
USHER SYNDROME, TYPE IIA; RETINAL DISEASE IN USHER SYNDROME TYPE IIA, MODIFIER OF
Identifiers:
MONDO: MONDO:0010169; MedGen: C1848634; Orphanet: 231178; Orphanet: 886; OMIM: 276901

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001253541Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001452249Natera, Inc.no assertion criteria providedBenign
(Sep 16, 2020)
germlineclinical testing

SCV001750420Nilou-Genome Labcriteria provided, single submitter
Benign
(Jul 1, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations.

Garcia-Garcia G, Aparisi MJ, Jaijo T, Rodrigo R, Leon AM, Avila-Fernandez A, Blanco-Kelly F, Bernal S, Navarro R, Diaz-Llopis M, Baiget M, Ayuso C, Millan JM, Aller E.

Orphanet J Rare Dis. 2011 Oct 17;6:65. doi: 10.1186/1750-1172-6-65.

PubMed [citation]
PMID:
22004887
PMCID:
PMC3207874

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV001253541.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001452249.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Nilou-Genome Lab, SCV001750420.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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