NM_001085382.2:c.1501G>A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001085382.2(PSAPL1):c.1501G>A(p.Ala501Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000605 in 1,487,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001085382.2 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSAPL1 | ENST00000319098.7 | c.1501G>A | p.Ala501Thr | missense_variant | Exon 1 of 1 | 6 | NM_001085382.2 | ENSP00000317445.4 | ||
SORCS2 | ENST00000507866.6 | c.548+37024C>T | intron_variant | Intron 2 of 26 | 1 | NM_020777.3 | ENSP00000422185.2 | |||
SORCS2 | ENST00000511199.1 | n.163+37024C>T | intron_variant | Intron 2 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152188Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000538 AC: 7AN: 130000 AF XY: 0.0000447 show subpopulations
GnomAD4 exome AF: 0.0000607 AC: 81AN: 1335406Hom.: 0 Cov.: 58 AF XY: 0.0000645 AC XY: 42AN XY: 650974 show subpopulations
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74348 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at