chr4-7433636-G-T
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_001085382.2(PSAPL1):c.1244C>A(p.Thr415Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,610,682 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 Uncertain significance (★).
Frequency
Consequence
NM_001085382.2 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSAPL1 | ENST00000319098.7 | c.1244C>A | p.Thr415Asn | missense_variant | Exon 1 of 1 | 6 | NM_001085382.2 | ENSP00000317445.4 | ||
SORCS2 | ENST00000507866.6 | c.548+37281G>T | intron_variant | Intron 2 of 26 | 1 | NM_020777.3 | ENSP00000422185.2 | |||
SORCS2 | ENST00000511199.1 | n.163+37281G>T | intron_variant | Intron 2 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00000817 AC: 2AN: 244938 AF XY: 0.0000150 show subpopulations
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458458Hom.: 0 Cov.: 63 AF XY: 0.00000965 AC XY: 7AN XY: 725160 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1244C>A (p.T415N) alteration is located in exon 1 (coding exon 1) of the PSAPL1 gene. This alteration results from a C to A substitution at nucleotide position 1244, causing the threonine (T) at amino acid position 415 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at