1-215879003-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_206933.4(USH2A):c.8319C>T(p.Ser2773=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000644 in 1,613,946 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S2773S) has been classified as Likely benign.
Frequency
Consequence
NM_206933.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.8319C>T | p.Ser2773= | synonymous_variant | 42/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.8319C>T | p.Ser2773= | synonymous_variant | 42/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000674083.1 | c.8319C>T | p.Ser2773= | synonymous_variant | 42/73 |
Frequencies
GnomAD3 genomes AF: 0.00365 AC: 555AN: 152080Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 263AN: 250048Hom.: 3 AF XY: 0.000754 AC XY: 102AN XY: 135238
GnomAD4 exome AF: 0.000330 AC: 482AN: 1461748Hom.: 5 Cov.: 32 AF XY: 0.000278 AC XY: 202AN XY: 727184
GnomAD4 genome AF: 0.00366 AC: 557AN: 152198Hom.: 2 Cov.: 32 AF XY: 0.00353 AC XY: 263AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 03, 2019 | - - |
Usher syndrome type 2A Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 08, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Ser2773Ser in Exon 42 of USH2A: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 1.4% (54/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs56829872). - |
Retinitis pigmentosa 39 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at