rs142481947
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The ENST00000307340.8(USH2A):c.11467G>A(p.Val3823Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,611,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V3823A) has been classified as Likely benign.
Frequency
Consequence
ENST00000307340.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.11467G>A | p.Val3823Ile | missense_variant | 59/72 | ENST00000307340.8 | NP_996816.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.11467G>A | p.Val3823Ile | missense_variant | 59/72 | 1 | NM_206933.4 | ENSP00000305941 | P1 | |
USH2A | ENST00000674083.1 | c.11467G>A | p.Val3823Ile | missense_variant | 59/73 | ENSP00000501296 |
Frequencies
GnomAD3 genomes AF: 0.00110 AC: 166AN: 150338Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.000302 AC: 76AN: 251424Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135880
GnomAD4 exome AF: 0.000111 AC: 162AN: 1461196Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 78AN XY: 726928
GnomAD4 genome AF: 0.00111 AC: 167AN: 150458Hom.: 0 Cov.: 26 AF XY: 0.000926 AC XY: 68AN XY: 73404
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 14, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 21, 2021 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.11467G>A (p.V3823I) alteration is located in exon 59 (coding exon 58) of the USH2A gene. This alteration results from a G to A substitution at nucleotide position 11467, causing the valine (V) at amino acid position 3823 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Retinal dystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Blueprint Genetics | Sep 26, 2018 | - - |
Usher syndrome type 2A Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 06, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 09, 2018 | p.Val3823Ile in exon 59 of USH2A: This variant is not expected to have clinical significance because it has been identified in 0.4% (45/10404) of African chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs142481947). 0.4% (95/23930) of African chromosomes by the Genome Aggr egation Database (gnomAD, http://gnomad.broadinstitute.org). - |
USH2A-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 22, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at