chr1-216323684-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_206933.4(USH2A):āc.1340A>Gā(p.Tyr447Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. Y447Y) has been classified as Likely benign.
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.1340A>G | p.Tyr447Cys | missense_variant | 8/72 | ENST00000307340.8 | |
USH2A | NM_007123.6 | c.1340A>G | p.Tyr447Cys | missense_variant | 8/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.1340A>G | p.Tyr447Cys | missense_variant | 8/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000366942.3 | c.1340A>G | p.Tyr447Cys | missense_variant | 8/21 | 1 | |||
USH2A | ENST00000674083.1 | c.1340A>G | p.Tyr447Cys | missense_variant | 8/73 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250118Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135206
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461238Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726926
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Sep 28, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at