chr1-215647649-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_206933.4(USH2A):c.14664G>A(p.Thr4888=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,614,016 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T4888T) has been classified as Likely benign.
Frequency
Consequence
NM_206933.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.14664G>A | p.Thr4888= | synonymous_variant | 67/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.14664G>A | p.Thr4888= | synonymous_variant | 67/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000674083.1 | c.14664G>A | p.Thr4888= | synonymous_variant | 67/73 |
Frequencies
GnomAD3 genomes AF: 0.000743 AC: 113AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000692 AC: 174AN: 251304Hom.: 0 AF XY: 0.000655 AC XY: 89AN XY: 135820
GnomAD4 exome AF: 0.00105 AC: 1531AN: 1461858Hom.: 1 Cov.: 31 AF XY: 0.00102 AC XY: 739AN XY: 727228
GnomAD4 genome AF: 0.000743 AC: 113AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.000821 AC XY: 61AN XY: 74326
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:6
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 29, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 16, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 19, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | USH2A: BP4, BP7 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Usher syndrome type 2A Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 08, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 17, 2014 | p.Thr4888Thr in exon 67 of USH2A: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. It has been identified in 0.1% (73/67624) of European ch romosomes by the Exome Aggregation Consortium (http://exac.broadinstitute.org; d bSNP rs111033525). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at