rs111033381
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_206933.4(USH2A):c.13297G>T(p.Val4433Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,614,142 control chromosomes in the GnomAD database, including 472 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 Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V4433V) has been classified as Likely benign.
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 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.13297G>T | p.Val4433Leu | missense_variant | Exon 63 of 72 | 1 | NM_206933.4 | ENSP00000305941.3 | ||
USH2A | ENST00000674083.1 | c.13297G>T | p.Val4433Leu | missense_variant | Exon 63 of 73 | ENSP00000501296.1 |
Frequencies
GnomAD3 genomes AF: 0.0182 AC: 2775AN: 152162Hom.: 46 Cov.: 32
GnomAD3 exomes AF: 0.0191 AC: 4802AN: 250872Hom.: 69 AF XY: 0.0188 AC XY: 2543AN XY: 135548
GnomAD4 exome AF: 0.0219 AC: 32020AN: 1461862Hom.: 426 Cov.: 31 AF XY: 0.0212 AC XY: 15446AN XY: 727226
GnomAD4 genome AF: 0.0182 AC: 2775AN: 152280Hom.: 46 Cov.: 32 AF XY: 0.0188 AC XY: 1397AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:3Other:1
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not specified Benign:3
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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