chr6-31138491-A-G

Position:

• chr6-31138491-A-G

Variant summary

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

The NM_014068.3(PSORS1C1):​c.43+32A>G variant causes a intron 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 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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]

PSORS1C1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.43+32A>G		intron_variant		ENST00000259881.10	NP_054787.2
PSORS1C2	NM_014069.3	c.56-185T>C		intron_variant		ENST00000259845.5	NP_054788.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.43+32A>G		intron_variant		1	NM_014068.3	ENSP00000259881.9
PSORS1C2	ENST00000259845.5	c.56-185T>C		intron_variant		1	NM_014069.3	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

GnomAD3 exomes AF: 0.329 AC: 81164 AN: 246496 Hom.: 14007 AF XY: 0.330 AC XY: 44397 AN XY: 134350

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 SAS exome AF: 0.299

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

Gnomad4 AFR exome AF: 0.455

Gnomad4 AMR exome AF: 0.294

Gnomad4 ASJ exome AF: 0.376

Gnomad4 EAS exome AF: 0.173

Gnomad4 SAS exome AF: 0.308

Gnomad4 FIN exome AF: 0.365

Gnomad4 NFE exome AF: 0.344

Gnomad4 OTH exome AF: 0.349

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

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.365

Alfa AF: 0.346 Hom.: 18768

Bravo AF: 0.368

Asia WGS AF: 0.251 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130573; hg19: chr6-31106268; COSMIC: COSV52535828; COSMIC: COSV52535828;