chr13-94462177-G-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 11P and 1B. PVS1PM2PP5BS1_Supporting
The NM_001922.5(DCT):c.876C>A(p.Tyr292Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,611,802 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_001922.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCT | NM_001922.5 | c.876C>A | p.Tyr292Ter | stop_gained | 5/8 | ENST00000377028.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCT | ENST00000377028.10 | c.876C>A | p.Tyr292Ter | stop_gained | 5/8 | 1 | NM_001922.5 | P1 | |
DCT | ENST00000446125.1 | c.876C>A | p.Tyr292Ter | stop_gained | 5/10 | 1 | |||
DCT | ENST00000490854.1 | n.638C>A | non_coding_transcript_exon_variant | 4/4 | 4 | ||||
DCT | ENST00000483392.6 | c.306C>A | p.Tyr102Ter | stop_gained, NMD_transcript_variant | 4/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151802Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251306Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135828
GnomAD4 exome AF: 0.000112 AC: 164AN: 1460000Hom.: 0 Cov.: 30 AF XY: 0.000114 AC XY: 83AN XY: 726472
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151802Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74100
ClinVar
Submissions by phenotype
Oculocutaneous albinism type 8 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 16, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at