6-31139410-G-A

Variant names:

• chr6-31139410-G-A
• rs1265093
• ENST00000552747.1:n.1105G>A

Variant summary

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

The ENST00000552747.1(PSORS1C1):​n.1105G>A 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 0.263 in 594,846 control chromosomes in the GnomAD database, including 21,562 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 0.25 (5046 hom., cov: 32)
  • Exomes 𝑓: 0.27 (16516 hom.)
• Consequence: PSORS1C1 ENST00000552747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 53 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 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.168-231G>A		intron	N/A	NP_054787.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	ENST00000552747.1	TSL:1	n.1105G>A		non_coding_transcript_exon	Exon 2 of 2
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.168-231G>A		intron	N/A	ENSP00000259881.9
	PSORS1C1	ENST00000479581.5	TSL:1	n.62-231G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38679 AN: 151994 Hom.: 5046 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.266 AC: 117978 AN: 442734 Hom.: 16516 Cov.: 4 AF XY: 0.264 AC XY: 61307 AN XY: 231990

African (AFR) AF: 0.195 AC: 2406 AN: 12340

American (AMR) AF: 0.326 AC: 6036 AN: 18510

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 1618 AN: 13628

East Asian (EAS) AF: 0.345 AC: 10696 AN: 30982

South Asian (SAS) AF: 0.256 AC: 11127 AN: 43420

European-Finnish (FIN) AF: 0.273 AC: 8098 AN: 29646

Middle Eastern (MID) AF: 0.220 AC: 428 AN: 1946

European-Non Finnish (NFE) AF: 0.266 AC: 70936 AN: 266440

Other (OTH) AF: 0.257 AC: 6633 AN: 25822

GnomAD4 genome AF: 0.254 AC: 38694 AN: 152112 Hom.: 5046 Cov.: 32 AF XY: 0.255 AC XY: 18985 AN XY: 74352

African (AFR) AF: 0.204 AC: 8482 AN: 41502

American (AMR) AF: 0.322 AC: 4914 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1762 AN: 5154

South Asian (SAS) AF: 0.251 AC: 1213 AN: 4826

European-Finnish (FIN) AF: 0.268 AC: 2841 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18314 AN: 67986

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.261 Hom.: 17319

Bravo AF: 0.256

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.72
PhyloP100		0.15
PromoterAI		0.021	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: rs1265093; hg19: chr6-31107187;