1-215934756-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_206933.4(USH2A):c.7160T>C(p.Met2387Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000731 in 1,612,662 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_206933.4 missense
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 |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.7160T>C | p.Met2387Thr | missense_variant | Exon 38 of 72 | 1 | NM_206933.4 | ENSP00000305941.3 | ||
USH2A | ENST00000674083.1 | c.7160T>C | p.Met2387Thr | missense_variant | Exon 38 of 73 | ENSP00000501296.1 |
Frequencies
GnomAD3 genomes AF: 0.00402 AC: 611AN: 152000Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.000973 AC: 244AN: 250850Hom.: 1 AF XY: 0.000590 AC XY: 80AN XY: 135554
GnomAD4 exome AF: 0.000388 AC: 566AN: 1460544Hom.: 0 Cov.: 31 AF XY: 0.000325 AC XY: 236AN XY: 726562
GnomAD4 genome AF: 0.00403 AC: 613AN: 152118Hom.: 6 Cov.: 32 AF XY: 0.00370 AC XY: 275AN XY: 74360
ClinVar
Submissions by phenotype
not specified Benign:3
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Met2387Thr in exon 38 of USH2A: This variant is not expected to have clinical si gnificance because it has been identified in 1.3% (50/3738) of African American chromosomes from a broad population by the NHLBI Exome sequencing project (http: //evs.gs.washington.edu/EVS/; dbSNP rs115015305). -
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not provided Benign:2
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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