15-65650550-G-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_004727.3(SLC24A1):c.2401G>T(p.Glu801Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,399,654 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_004727.3 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 |
---|---|---|---|---|---|---|---|
SLC24A1 | NM_004727.3 | c.2401G>T | p.Glu801Ter | stop_gained | 7/10 | ENST00000261892.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC24A1 | ENST00000261892.11 | c.2401G>T | p.Glu801Ter | stop_gained | 7/10 | 1 | NM_004727.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000641 AC: 1AN: 156086Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82242
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399654Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 690334
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Congenital stationary night blindness 1D Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at