rs3130558

Positions:

• chr6-31129406-C-G

Variant summary

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

The NM_014068.3(PSORS1C1):​c.-64-163C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,114 control chromosomes in the GnomAD database, including 45,504 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 0.77 (45504 hom., cov: 31)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSORS1C1	NM_014068.3	c.-64-163C>G		intron_variant		ENST00000259881.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-64-163C>G		intron_variant		1	NM_014068.3	P2

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116941 AN: 151996 Hom.: 45468 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.769

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.769 AC: 117030 AN: 152114 Hom.: 45504 Cov.: 31 AF XY: 0.767 AC XY: 56985 AN XY: 74344

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.768

Alfa AF: 0.748 Hom.: 23676

Bravo AF: 0.780

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.8
DANN	Benign	0.70

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: rs3130558; hg19: chr6-31097183;