rs2233952
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014069.3(PSORS1C2):c.248T>C(p.Leu83Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 1,603,552 control chromosomes in the GnomAD database, including 635,038 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014069.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSORS1C2 | NM_014069.3 | c.248T>C | p.Leu83Pro | missense_variant | 2/2 | ENST00000259845.5 | |
PSORS1C1 | NM_014068.3 | c.14-316A>G | intron_variant | ENST00000259881.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSORS1C2 | ENST00000259845.5 | c.248T>C | p.Leu83Pro | missense_variant | 2/2 | 1 | NM_014069.3 | P1 | |
PSORS1C1 | ENST00000259881.10 | c.14-316A>G | intron_variant | 1 | NM_014068.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.918 AC: 139496AN: 151896Hom.: 64187 Cov.: 29
GnomAD3 exomes AF: 0.903 AC: 213828AN: 236744Hom.: 96805 AF XY: 0.904 AC XY: 117075AN XY: 129532
GnomAD4 exome AF: 0.886 AC: 1286203AN: 1451538Hom.: 570788 Cov.: 47 AF XY: 0.888 AC XY: 640765AN XY: 721780
GnomAD4 genome ? AF: 0.918 AC: 139621AN: 152014Hom.: 64250 Cov.: 29 AF XY: 0.918 AC XY: 68220AN XY: 74276
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at