rs1265093

chr6-31139410-G-A

Variant summary

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

The NM_014068.3(PSORS1C1):c.168-231G>A variant causes a intron 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 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSORS1C1	NM_014068.3	c.168-231G>A		intron_variant		ENST00000259881.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.168-231G>A		intron_variant		1	NM_014068.3	P2

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

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.326

Gnomad4 ASJ exome AF: 0.119

Gnomad4 EAS exome AF: 0.345

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.266

Gnomad4 OTH exome AF: 0.257

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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.226

Alfa AF: 0.257 Hom.: 6322

Bravo AF: 0.256

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.3
Dann	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs1265093; hg19: chr6-31107187;