chr17-74922974-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173477.5(USH1G):c.100A>T(p.Thr34Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000142 in 1,403,672 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T34N) has been classified as Uncertain significance.
Frequency
Consequence
NM_173477.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH1G | NM_173477.5 | c.100A>T | p.Thr34Ser | missense_variant | 1/3 | ENST00000614341.5 | |
USH1G | NM_001282489.3 | c.-157A>T | 5_prime_UTR_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1G | ENST00000614341.5 | c.100A>T | p.Thr34Ser | missense_variant | 1/3 | 1 | NM_173477.5 | P1 | |
OTOP2 | ENST00000580223.2 | c.-291T>A | 5_prime_UTR_variant | 1/5 | 1 | ||||
USH1G | ENST00000579243.1 | c.100A>T | p.Thr34Ser | missense_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000591 AC: 1AN: 169160Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 90068
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1403672Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 692338
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.100A>T (p.T34S) alteration is located in exon 1 (coding exon 1) of the USH1G gene. This alteration results from a A to T substitution at nucleotide position 100, causing the threonine (T) at amino acid position 34 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at