6-31137856-C-T

Variant names:

• chr6-31137856-C-T
• rs2074478
• NM_014069.3:c.*95G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014069.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C2	NM_014069.3	MANE Select	c.*95G>A		3_prime_UTR	Exon 2 of 2	NP_054788.2	Q9UIG4
	PSORS1C1	NM_014068.3	MANE Select	c.14-574C>T		intron	N/A	NP_054787.2	Q9UIG5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C2	ENST00000259845.5	TSL:1 MANE Select	c.*95G>A		3_prime_UTR	Exon 2 of 2	ENSP00000259845.4	Q9UIG4
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.14-574C>T		intron	N/A	ENSP00000259881.9	Q9UIG5-1
	PSORS1C1	ENST00000479581.5	TSL:1	n.62-1785C>T		intron	N/A

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

African (AFR) AF: 0.892 AC: 9121 AN: 10220

American (AMR) AF: 0.845 AC: 9971 AN: 11804

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 10847 AN: 11510

East Asian (EAS) AF: 0.775 AC: 20303 AN: 26192

South Asian (SAS) AF: 0.801 AC: 19111 AN: 23858

European-Finnish (FIN) AF: 0.799 AC: 31295 AN: 39154

Middle Eastern (MID) AF: 0.858 AC: 1505 AN: 1754

European-Non Finnish (NFE) AF: 0.813 AC: 210261 AN: 258598

Other (OTH) AF: 0.830 AC: 18859 AN: 22716

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

African (AFR) AF: 0.884 AC: 36712 AN: 41542

American (AMR) AF: 0.856 AC: 13086 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3260 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3925 AN: 5164

South Asian (SAS) AF: 0.814 AC: 3925 AN: 4824

European-Finnish (FIN) AF: 0.807 AC: 8546 AN: 10588

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55513 AN: 68000

Other (OTH) AF: 0.854 AC: 1805 AN: 2114

Alfa AF: 0.827 Hom.: 213351

Bravo AF: 0.845

Asia WGS AF: 0.800 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.73
PhyloP100		-3.1
PromoterAI		-0.030	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2074478; hg19: chr6-31105633;