chr12-107708927-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007062.3(PWP1):c.1079C>T(p.Ala360Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000246 in 1,612,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007062.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PWP1 | NM_007062.3 | c.1079C>T | p.Ala360Val | missense_variant, splice_region_variant | Exon 12 of 15 | ENST00000412830.8 | NP_008993.1 | |
PWP1 | NM_001317962.2 | c.893C>T | p.Ala298Val | missense_variant, splice_region_variant | Exon 12 of 15 | NP_001304891.1 | ||
PWP1 | NM_001317963.2 | c.443C>T | p.Ala148Val | missense_variant, splice_region_variant | Exon 12 of 15 | NP_001304892.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PWP1 | ENST00000412830.8 | c.1079C>T | p.Ala360Val | missense_variant, splice_region_variant | Exon 12 of 15 | 1 | NM_007062.3 | ENSP00000387365.3 | ||
PWP1 | ENST00000541166.1 | c.893C>T | p.Ala298Val | missense_variant, splice_region_variant | Exon 12 of 15 | 2 | ENSP00000445249.1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 54AN: 250868Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135592
GnomAD4 exome AF: 0.000251 AC: 366AN: 1460434Hom.: 0 Cov.: 31 AF XY: 0.000233 AC XY: 169AN XY: 726580
GnomAD4 genome AF: 0.000204 AC: 31AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1079C>T (p.A360V) alteration is located in exon 12 (coding exon 12) of the PWP1 gene. This alteration results from a C to T substitution at nucleotide position 1079, causing the alanine (A) at amino acid position 360 to be replaced by a valine (V). 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