ENST00000552747.1:n.186A>G

Variant names:

• chr6-31138491-A-G
• rs3130573
• ENST00000552747.1:n.186A>G

Variant summary

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

The ENST00000552747.1(PSORS1C1):​n.186A>G 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 0.343 in 1,609,828 control chromosomes in the GnomAD database, including 96,815 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 0.37 (10630 hom., cov: 29)
  • Exomes 𝑓: 0.34 (86185 hom.)
• Consequence: PSORS1C1 ENST00000552747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 74 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 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.43+32A>G		intron	N/A	NP_054787.2
	PSORS1C2	NM_014069.3	MANE Select	c.56-185T>C		intron	N/A	NP_054788.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	ENST00000552747.1	TSL:1	n.186A>G		non_coding_transcript_exon	Exon 2 of 2
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.43+32A>G		intron	N/A	ENSP00000259881.9
	PSORS1C2	ENST00000259845.5	TSL:1 MANE Select	c.56-185T>C		intron	N/A	ENSP00000259845.4

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56063 AN: 151572 Hom.: 10615 Cov.: 29

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.368

GnomAD2 exomes AF: 0.329 AC: 81164 AN: 246496 AF XY: 0.330

Gnomad AFR exome AF: 0.450

Gnomad AMR exome AF: 0.291

Gnomad ASJ exome AF: 0.371

Gnomad EAS exome AF: 0.188

Gnomad FIN exome AF: 0.363

Gnomad NFE exome AF: 0.346

Gnomad OTH exome AF: 0.326

GnomAD4 exome AF: 0.340 AC: 495315 AN: 1458136 Hom.: 86185 Cov.: 36 AF XY: 0.340 AC XY: 246487 AN XY: 725540

African (AFR) AF: 0.455 AC: 15220 AN: 33430

American (AMR) AF: 0.294 AC: 13160 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 9815 AN: 26120

East Asian (EAS) AF: 0.173 AC: 6879 AN: 39696

South Asian (SAS) AF: 0.308 AC: 26524 AN: 86208

European-Finnish (FIN) AF: 0.365 AC: 19068 AN: 52306

Middle Eastern (MID) AF: 0.330 AC: 1902 AN: 5762

European-Non Finnish (NFE) AF: 0.344 AC: 381733 AN: 1109622

Other (OTH) AF: 0.349 AC: 21014 AN: 60278

GnomAD4 genome AF: 0.370 AC: 56126 AN: 151692 Hom.: 10630 Cov.: 29 AF XY: 0.368 AC XY: 27260 AN XY: 74102

African (AFR) AF: 0.450 AC: 18575 AN: 41302

American (AMR) AF: 0.301 AC: 4597 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1022 AN: 5144

South Asian (SAS) AF: 0.337 AC: 1612 AN: 4782

European-Finnish (FIN) AF: 0.377 AC: 3982 AN: 10552

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23721 AN: 67874

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.351 Hom.: 42465

Bravo AF: 0.368

Asia WGS AF: 0.251 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		0.083
PromoterAI		-0.0021	Neutral
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3130573; hg19: chr6-31106268; COSMIC: COSV52535828; COSMIC: COSV52535828;