chr1-215779946-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_206933.4(USH2A):c.10836C>A(p.Val3612Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 1,614,020 control chromosomes in the GnomAD database, including 375 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_206933.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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USH2A | ENST00000307340.8 | c.10836C>A | p.Val3612Val | synonymous_variant | Exon 55 of 72 | 1 | NM_206933.4 | ENSP00000305941.3 | ||
USH2A | ENST00000674083.1 | c.10836C>A | p.Val3612Val | synonymous_variant | Exon 55 of 73 | ENSP00000501296.1 |
Frequencies
GnomAD3 genomes AF: 0.0271 AC: 4125AN: 152020Hom.: 197 Cov.: 32
GnomAD3 exomes AF: 0.00717 AC: 1803AN: 251374Hom.: 76 AF XY: 0.00504 AC XY: 684AN XY: 135848
GnomAD4 exome AF: 0.00274 AC: 4007AN: 1461882Hom.: 178 Cov.: 32 AF XY: 0.00235 AC XY: 1708AN XY: 727242
GnomAD4 genome AF: 0.0272 AC: 4136AN: 152138Hom.: 197 Cov.: 32 AF XY: 0.0255 AC XY: 1895AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Benign:2
Val3612Val in exon 55 of USH2A: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located near a splice junction and is listed in dbSNP (rs61276761, 5/50 Black chromosomes). -
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Usher syndrome type 2A Benign:2
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Retinitis pigmentosa 39 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at