rs59174500
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP4_StrongBP6_Very_StrongBS2
The ENST00000307340.8(USH2A):c.8458G>A(p.Val2820Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000688 in 1,614,010 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000307340.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.8458G>A | p.Val2820Ile | missense_variant | 42/72 | ENST00000307340.8 | NP_996816.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.8458G>A | p.Val2820Ile | missense_variant | 42/72 | 1 | NM_206933.4 | ENSP00000305941 | P1 | |
USH2A | ENST00000674083.1 | c.8458G>A | p.Val2820Ile | missense_variant | 42/73 | ENSP00000501296 |
Frequencies
GnomAD3 genomes AF: 0.00364 AC: 554AN: 152076Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00104 AC: 262AN: 251214Hom.: 3 AF XY: 0.000722 AC XY: 98AN XY: 135784
GnomAD4 exome AF: 0.000380 AC: 555AN: 1461816Hom.: 5 Cov.: 32 AF XY: 0.000327 AC XY: 238AN XY: 727206
GnomAD4 genome AF: 0.00365 AC: 556AN: 152194Hom.: 2 Cov.: 32 AF XY: 0.00348 AC XY: 259AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 03, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Usher syndrome type 2A Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 08, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Val2820Ile in Exon 42 of USH2A: This variant is not expected to have clinical si gnificance because it has been identified in 1.4% (54/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs59174500). - |
Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 20, 2022 | - - |
Retinitis pigmentosa 39 Benign:1
Likely 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