chr15-76994821-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001321137.1(PSTPIP1):c.26+6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000349 in 1,289,008 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001321137.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSTPIP1 | ENST00000559785.5 | n.26+6C>T | splice_region_variant, intron_variant | Intron 1 of 15 | 1 | ENSP00000452986.1 | ||||
PSTPIP1 | ENST00000558407.5 | c.26+6C>T | splice_region_variant, intron_variant | Intron 2 of 6 | 3 | ENSP00000453268.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000781 AC: 10AN: 128090Hom.: 0 AF XY: 0.0000713 AC XY: 5AN XY: 70140
GnomAD4 exome AF: 0.0000343 AC: 39AN: 1136872Hom.: 1 Cov.: 30 AF XY: 0.0000287 AC XY: 16AN XY: 557696
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74308
ClinVar
Submissions by phenotype
PSTPIP1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at