chr6-31137856-C-T

Position:

• chr6-31137856-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014069.3(PSORS1C2):​c.*95G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 558,006 control chromosomes in the GnomAD database, including 189,542 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.84 (53876 hom., cov: 31)
  • Exomes 𝑓: 0.82 (135666 hom.)
• Consequence: PSORS1C2 NM_014069.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11

Genes affected

PSORS1C2 (HGNC:17199): (psoriasis susceptibility 1 candidate 2) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PSORS1C1 (HGNC:17202): (psoriasis susceptibility 1 candidate 1) This gene is one of several genes thought to confer susceptibility to psoriasis and systemic sclerosis, located on chromosome 6 near the major histocompatibility complex (MHC) class I region. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSORS1C2	NM_014069.3	c.*95G>A		3_prime_UTR_variant	2/2	ENST00000259845.5
PSORS1C1	NM_014068.3	c.14-574C>T		intron_variant		ENST00000259881.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSORS1C2	ENST00000259845.5	c.*95G>A		3_prime_UTR_variant	2/2	1	NM_014069.3	P1
PSORS1C1	ENST00000259881.10	c.14-574C>T		intron_variant		1	NM_014068.3	P2

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127782 AN: 152082 Hom.: 53828 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.853

GnomAD4 exome AF: 0.816 AC: 331273 AN: 405806 Hom.: 135666 Cov.: 6 AF XY: 0.816 AC XY: 169405 AN XY: 207630

Gnomad4 AFR exome AF: 0.892

Gnomad4 AMR exome AF: 0.845

Gnomad4 ASJ exome AF: 0.942

Gnomad4 EAS exome AF: 0.775

Gnomad4 SAS exome AF: 0.801

Gnomad4 FIN exome AF: 0.799

Gnomad4 NFE exome AF: 0.813

Gnomad4 OTH exome AF: 0.830

GnomAD4 genome AF: 0.840 AC: 127894 AN: 152200 Hom.: 53876 Cov.: 31 AF XY: 0.839 AC XY: 62440 AN XY: 74408

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.854

Alfa AF: 0.826 Hom.: 95472

Bravo AF: 0.845

Asia WGS AF: 0.800 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2074478; hg19: chr6-31105633;