rs141671082
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM5BP4_StrongBP6_Very_StrongBS2
The NM_206933.4(USH2A):āc.4543A>Gā(p.Thr1515Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000542 in 1,613,848 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1515M) has been classified as Likely pathogenic.
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.4543A>G | p.Thr1515Ala | missense_variant | 21/72 | ENST00000307340.8 | NP_996816.3 | |
USH2A | NM_007123.6 | c.4543A>G | p.Thr1515Ala | missense_variant | 21/21 | NP_009054.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.4543A>G | p.Thr1515Ala | missense_variant | 21/72 | 1 | NM_206933.4 | ENSP00000305941 | P1 | |
USH2A | ENST00000366942.3 | c.4543A>G | p.Thr1515Ala | missense_variant | 21/21 | 1 | ENSP00000355909 | |||
USH2A | ENST00000674083.1 | c.4543A>G | p.Thr1515Ala | missense_variant | 21/73 | ENSP00000501296 |
Frequencies
GnomAD3 genomes AF: 0.00302 AC: 460AN: 152166Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.000810 AC: 203AN: 250662Hom.: 0 AF XY: 0.000568 AC XY: 77AN XY: 135458
GnomAD4 exome AF: 0.000283 AC: 414AN: 1461564Hom.: 1 Cov.: 31 AF XY: 0.000239 AC XY: 174AN XY: 727088
GnomAD4 genome AF: 0.00303 AC: 461AN: 152284Hom.: 4 Cov.: 33 AF XY: 0.00287 AC XY: 214AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 13, 2013 | Thr1515Ala in Exon 21A of USH2A: This variant is not expected to have clinical s ignificance because it has been identified in 1.1% (48/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs141671082). In addition, the threonine (Th r) residue at position 1515 is poorly conserved across species with several mam mals (rat, mouse, kangaroo rat) having an alanine (Ala) at this position. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 12, 2019 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Usher syndrome type 2A Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 18, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Retinitis pigmentosa 39 Benign:1
Likely 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