rs75397806
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_206933.4(USH2A):c.10552G>A(p.Val3518Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,613,870 control chromosomes in the GnomAD database, including 23 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 (★★).
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.10552G>A | p.Val3518Ile | missense_variant | 53/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.10552G>A | p.Val3518Ile | missense_variant | 53/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000674083.1 | c.10552G>A | p.Val3518Ile | missense_variant | 53/73 |
Frequencies
GnomAD3 genomes ? AF: 0.00633 AC: 963AN: 152136Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00159 AC: 400AN: 251158Hom.: 8 AF XY: 0.00117 AC XY: 159AN XY: 135742
GnomAD4 exome AF: 0.000607 AC: 887AN: 1461616Hom.: 15 Cov.: 31 AF XY: 0.000507 AC XY: 369AN XY: 727114
GnomAD4 genome ? AF: 0.00636 AC: 968AN: 152254Hom.: 8 Cov.: 33 AF XY: 0.00588 AC XY: 438AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 08, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 07, 2011 | Val3518Ile in exon 53 of USH2A: This variant is not expected to have clinical si gnificance because it has been identified in over 1% of controls (rs75397806). - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 17, 2018 | This variant is associated with the following publications: (PMID: 28838317) - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Usher syndrome type 2A Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 06, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Retinitis pigmentosa 39 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