rs696723
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_206933.4(USH2A):āc.2137G>Cā(p.Gly713Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0202 in 1,613,916 control chromosomes in the GnomAD database, including 1,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. G713G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.2137G>C | p.Gly713Arg | missense_variant | 12/72 | ENST00000307340.8 | |
USH2A | NM_007123.6 | c.2137G>C | p.Gly713Arg | missense_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.2137G>C | p.Gly713Arg | missense_variant | 12/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000366942.3 | c.2137G>C | p.Gly713Arg | missense_variant | 12/21 | 1 | |||
USH2A | ENST00000674083.1 | c.2137G>C | p.Gly713Arg | missense_variant | 12/73 |
Frequencies
GnomAD3 genomes ? AF: 0.0576 AC: 8754AN: 152066Hom.: 654 Cov.: 32
GnomAD3 exomes AF: 0.0232 AC: 5814AN: 250936Hom.: 296 AF XY: 0.0207 AC XY: 2811AN XY: 135614
GnomAD4 exome AF: 0.0163 AC: 23891AN: 1461732Hom.: 779 Cov.: 32 AF XY: 0.0159 AC XY: 11536AN XY: 727172
GnomAD4 genome ? AF: 0.0576 AC: 8765AN: 152184Hom.: 655 Cov.: 32 AF XY: 0.0563 AC XY: 4186AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:4Other:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided, no classification provided | literature only | NEI Ophthalmic Genomics Laboratory, National Institutes of Health | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 30245029, 15325563, 15241801, 22952768, 27884173, 10909849, 21228398, 22004887, 20981092, 21738395, 14676276, 22025579, 12112664, 25262649) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 15, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 19, 2008 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 18, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
Usher syndrome type 2A Benign:4
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | curation | SIB Swiss Institute of Bioinformatics | May 31, 2018 | This variant is interpreted as a Benign - Stand Alone, for Usher syndrome 2A (autosomal recessive, mild), in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BS4 => Lack of segregation in affected members of a family (PMID:15325563). BA1 => Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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. - |
Retinitis pigmentosa 39 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Retinitis pigmentosa Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at