chr22-19176262-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_005984.5(SLC25A1):c.822-18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,509,666 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 Likely benign (★★).
Frequency
Consequence
NM_005984.5 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.822-18G>A | intron_variant | Intron 8 of 8 | ENST00000215882.10 | NP_005975.1 | ||
SLC25A1 | NM_001256534.2 | c.843-18G>A | intron_variant | Intron 7 of 7 | NP_001243463.1 | |||
SLC25A1 | NM_001287387.2 | c.513-18G>A | intron_variant | Intron 8 of 8 | NP_001274316.1 | |||
SLC25A1 | NR_046298.3 | n.746-18G>A | intron_variant | Intron 7 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.822-18G>A | intron_variant | Intron 8 of 8 | 1 | NM_005984.5 | ENSP00000215882.5 | |||
SLC25A1 | ENST00000451283.5 | c.513-18G>A | intron_variant | Intron 8 of 8 | 2 | ENSP00000401480.1 | ||||
SLC25A1 | ENST00000470922.5 | n.964-18G>A | intron_variant | Intron 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248964Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134976
GnomAD4 exome AF: 0.0000199 AC: 27AN: 1357824Hom.: 0 Cov.: 27 AF XY: 0.0000162 AC XY: 11AN XY: 680992
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74176
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at