rs147967199
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_173477.5(USH1G):āc.715A>Cā(p.Lys239Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,603,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K239N) has been classified as Uncertain significance.
Frequency
Consequence
NM_173477.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH1G | NM_173477.5 | c.715A>C | p.Lys239Gln | missense_variant | 2/3 | ENST00000614341.5 | |
USH1G | NM_001282489.3 | c.406A>C | p.Lys136Gln | missense_variant | 2/3 | ||
USH1G | XM_011524296.2 | c.406A>C | p.Lys136Gln | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1G | ENST00000614341.5 | c.715A>C | p.Lys239Gln | missense_variant | 2/3 | 1 | NM_173477.5 | P1 | |
USH1G | ENST00000579243.1 | c.*314A>C | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000913 AC: 139AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000249 AC: 60AN: 240552Hom.: 0 AF XY: 0.000175 AC XY: 23AN XY: 131562
GnomAD4 exome AF: 0.0000917 AC: 133AN: 1450740Hom.: 0 Cov.: 42 AF XY: 0.0000692 AC XY: 50AN XY: 722236
GnomAD4 genome AF: 0.000912 AC: 139AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.000966 AC XY: 72AN XY: 74500
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 15, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 10, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 20, 2017 | p.Lys239Gln in exon 2 of USH1G: This variant is not expected to have clinical si gnificance because it has been identified in 0.3% (81/23730) of African chromoso mes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org ; dbSNP rs147967199). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at