chr2-44312754-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_ModeratePM2PP3_Strong
The NM_000341.4(SLC3A1):c.1500+1G>A variant causes a splice donor change. The variant allele was found at a frequency of 0.00000675 in 148,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000341.4 splice_donor
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A1 | NM_000341.4 | c.1500+1G>A | splice_donor_variant | ENST00000260649.11 | |||
SLC3A1 | XM_011533047.4 | c.1500+1G>A | splice_donor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A1 | ENST00000260649.11 | c.1500+1G>A | splice_donor_variant | 1 | NM_000341.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000675 AC: 1AN: 148158Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000675 AC: 1AN: 148158Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at