17-74920326-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_173477.5(USH1G):āc.510C>Gā(p.Ala170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000721 in 1,608,952 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A170A) has been classified as Likely benign.
Frequency
Consequence
NM_173477.5 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 |
---|---|---|---|---|---|---|---|
USH1G | NM_173477.5 | c.510C>G | p.Ala170= | synonymous_variant | 2/3 | ENST00000614341.5 | |
USH1G | NM_001282489.3 | c.201C>G | p.Ala67= | synonymous_variant | 2/3 | ||
USH1G | XM_011524296.2 | c.201C>G | p.Ala67= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1G | ENST00000614341.5 | c.510C>G | p.Ala170= | synonymous_variant | 2/3 | 1 | NM_173477.5 | P1 | |
USH1G | ENST00000579243.1 | c.*109C>G | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000142 AC: 35AN: 246188Hom.: 0 AF XY: 0.000142 AC XY: 19AN XY: 133884
GnomAD4 exome AF: 0.0000755 AC: 110AN: 1456700Hom.: 2 Cov.: 42 AF XY: 0.0000856 AC XY: 62AN XY: 724546
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74378
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 08, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | USH1G: BP4, BP7 - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 25, 2011 | Ala170Ala in exon 2 of USH1G: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located near a splice junction. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
USH1G-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at