ENST00000552747.1:n.1005T>C

Variant names:

• chr6-31139310-T-C
• rs3094663
• ENST00000552747.1:n.1005T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000552747.1(PSORS1C1):​n.1005T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 582,388 control chromosomes in the GnomAD database, including 148,791 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 0.72 (39573 hom., cov: 31)
  • Exomes 𝑓: 0.71 (109218 hom.)
• Consequence: PSORS1C1 ENST00000552747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 55 publications found

Genes affected

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552747.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	NM_014068.3	MANE Select	c.168-331T>C		intron	N/A	NP_054787.2
	PSORS1C2	NM_014069.3	MANE Select	c.-284A>G		upstream_gene	N/A	NP_054788.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	ENST00000552747.1	TSL:1	n.1005T>C		non_coding_transcript_exon	Exon 2 of 2
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.168-331T>C		intron	N/A	ENSP00000259881.9
	PSORS1C1	ENST00000479581.5	TSL:1	n.62-331T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109644 AN: 151888 Hom.: 39538 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.749

GnomAD4 exome AF: 0.710 AC: 305752 AN: 430382 Hom.: 109218 Cov.: 2 AF XY: 0.709 AC XY: 159470 AN XY: 225032

African (AFR) AF: 0.743 AC: 9075 AN: 12212

American (AMR) AF: 0.746 AC: 13283 AN: 17796

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 9848 AN: 13448

East Asian (EAS) AF: 0.710 AC: 21732 AN: 30616

South Asian (SAS) AF: 0.708 AC: 28878 AN: 40794

European-Finnish (FIN) AF: 0.708 AC: 20676 AN: 29218

Middle Eastern (MID) AF: 0.777 AC: 1487 AN: 1914

European-Non Finnish (NFE) AF: 0.705 AC: 182585 AN: 259118

Other (OTH) AF: 0.720 AC: 18188 AN: 25266

GnomAD4 genome AF: 0.722 AC: 109732 AN: 152006 Hom.: 39573 Cov.: 31 AF XY: 0.723 AC XY: 53704 AN XY: 74316

African (AFR) AF: 0.750 AC: 31078 AN: 41444

American (AMR) AF: 0.739 AC: 11282 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2447 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3610 AN: 5144

South Asian (SAS) AF: 0.687 AC: 3307 AN: 4816

European-Finnish (FIN) AF: 0.709 AC: 7495 AN: 10572

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47997 AN: 67976

Other (OTH) AF: 0.747 AC: 1576 AN: 2110

Alfa AF: 0.714 Hom.: 160501

Bravo AF: 0.727

Asia WGS AF: 0.738 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.83
PhyloP100		0.13
PromoterAI		-0.0063	Neutral
Mutation Taster		=299/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs3094663; hg19: chr6-31107087; COSMIC: COSV105012261; COSMIC: COSV105012261;