9-111727693-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001378211.1(SHOC1):c.1774C>T(p.Arg592Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000872 in 1,606,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001378211.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOC1 | NM_001378211.1 | c.1774C>T | p.Arg592Ter | stop_gained | 13/28 | ENST00000682961.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOC1 | ENST00000682961.1 | c.1774C>T | p.Arg592Ter | stop_gained | 13/28 | NM_001378211.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244332Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131876
GnomAD4 exome AF: 0.00000688 AC: 10AN: 1454348Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 723112
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 33 AF XY: 0.0000405 AC XY: 3AN XY: 74160
ClinVar
Submissions by phenotype
Spermatogenic failure 75 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at