rs111033397
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_206933.4(USH2A):c.9213G>A(p.Ser3071=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,613,708 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S3071S) has been classified as Likely benign.
Frequency
Consequence
NM_206933.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.9213G>A | p.Ser3071= | synonymous_variant | 46/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.9213G>A | p.Ser3071= | synonymous_variant | 46/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000674083.1 | c.9213G>A | p.Ser3071= | synonymous_variant | 46/73 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1576AN: 152148Hom.: 18 Cov.: 33
GnomAD3 exomes AF: 0.00304 AC: 763AN: 250628Hom.: 8 AF XY: 0.00242 AC XY: 328AN XY: 135440
GnomAD4 exome AF: 0.00143 AC: 2093AN: 1461442Hom.: 29 Cov.: 31 AF XY: 0.00131 AC XY: 950AN XY: 727012
GnomAD4 genome ? AF: 0.0104 AC: 1578AN: 152266Hom.: 18 Cov.: 33 AF XY: 0.00999 AC XY: 744AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 10, 2011 | Ser3071Ser in exon 46 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 was identified in 6/118 (5%) Black individuals (rs11103339 7). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 12, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
Usher syndrome type 2A Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
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