rs141489104
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBS2_Supporting
The NM_206933.4(USH2A):c.2094C>T(p.Thr698=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000217 in 1,614,052 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T698T) 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.2094C>T | p.Thr698= | synonymous_variant | 12/72 | ENST00000307340.8 | |
USH2A | NM_007123.6 | c.2094C>T | p.Thr698= | synonymous_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.2094C>T | p.Thr698= | synonymous_variant | 12/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000366942.3 | c.2094C>T | p.Thr698= | synonymous_variant | 12/21 | 1 | |||
USH2A | ENST00000674083.1 | c.2094C>T | p.Thr698= | synonymous_variant | 12/73 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 183AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000327 AC: 82AN: 250906Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135580
GnomAD4 exome AF: 0.000115 AC: 168AN: 1461776Hom.: 2 Cov.: 32 AF XY: 0.000103 AC XY: 75AN XY: 727188
GnomAD4 genome AF: 0.00120 AC: 183AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.00110 AC XY: 82AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 22, 2016 | p.Thr698Thr in Exon 12 of USH2A: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 0.5% (48/10398) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broad institute.org; dbSNP rs141489104). - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 03, 2016 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 30, 2020 | - - |
Retinitis pigmentosa 39 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Usher syndrome type 2A 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