6-31138682-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014068.3(PSORS1C1):c.70C>A(p.Pro24Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,612,958 control chromosomes in the GnomAD database, including 9,966 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014068.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSORS1C1 | NM_014068.3 | c.70C>A | p.Pro24Thr | missense_variant | 5/6 | ENST00000259881.10 | |
PSORS1C2 | NM_014069.3 | c.55+290G>T | intron_variant | ENST00000259845.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSORS1C1 | ENST00000259881.10 | c.70C>A | p.Pro24Thr | missense_variant | 5/6 | 1 | NM_014068.3 | P2 | |
PSORS1C2 | ENST00000259845.5 | c.55+290G>T | intron_variant | 1 | NM_014069.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.121 AC: 18385AN: 151702Hom.: 1231 Cov.: 30
GnomAD3 exomes AF: 0.130 AC: 31989AN: 246934Hom.: 2457 AF XY: 0.128 AC XY: 17175AN XY: 134446
GnomAD4 exome AF: 0.100 AC: 146719AN: 1461138Hom.: 8734 Cov.: 54 AF XY: 0.101 AC XY: 73541AN XY: 726876
GnomAD4 genome AF: 0.121 AC: 18403AN: 151820Hom.: 1232 Cov.: 30 AF XY: 0.124 AC XY: 9209AN XY: 74180
ClinVar
Submissions by phenotype
PSORS1C1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 2019 | This variant is classified as 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