rs111033498
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_206933.4(USH2A):c.14960C>T(p.Ala4987Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00219 in 1,613,720 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A4987A) has been classified as Uncertain significance.
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.14960C>T | p.Ala4987Val | missense_variant | 68/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.14960C>T | p.Ala4987Val | missense_variant | 68/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000674083.1 | c.14960C>T | p.Ala4987Val | missense_variant | 68/73 |
Frequencies
GnomAD3 genomes ? AF: 0.00614 AC: 933AN: 151838Hom.: 29 Cov.: 31
GnomAD3 exomes AF: 0.00690 AC: 1723AN: 249782Hom.: 57 AF XY: 0.00523 AC XY: 706AN XY: 135110
GnomAD4 exome AF: 0.00177 AC: 2586AN: 1461764Hom.: 87 Cov.: 32 AF XY: 0.00149 AC XY: 1085AN XY: 727192
GnomAD4 genome ? AF: 0.00620 AC: 942AN: 151956Hom.: 29 Cov.: 31 AF XY: 0.00703 AC XY: 522AN XY: 74256
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 11, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 12, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 05, 2011 | Ala4987Val in exon 68 of USH2A: This variant is not expected to have clinical si gnificance because this residue is not highly conserved across species. Of note, chicken and frog have an aspartic acid at this position. In addition, the varia nt has been identified by our laboratory in 5/223 (2.3%) probands including 3/31 (9.7%) Hispanic probands. - |
Retinitis pigmentosa 39 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Usher syndrome type 2A 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