rs3131009

Variant names:

• chr6-31131055-G-A
• rs3131009
• NM_014068.3:c.13+1410G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31131055-G-A
• chr6-31131055-G-C
• chr6-31131055-G-T

Variant summary

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

The NM_014068.3(PSORS1C1):​c.13+1410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 151,720 control chromosomes in the GnomAD database, including 44,680 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 0.76 (44680 hom., cov: 28)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 27 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.13+1410G>A		intron_variant	Intron 3 of 5	ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.13+1410G>A		intron_variant	Intron 3 of 5	1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115756 AN: 151602 Hom.: 44644 Cov.: 28

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.764 AC: 115845 AN: 151720 Hom.: 44680 Cov.: 28 AF XY: 0.762 AC XY: 56434 AN XY: 74104

African (AFR) AF: 0.859 AC: 35569 AN: 41386

American (AMR) AF: 0.736 AC: 11221 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2835 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4520 AN: 5148

South Asian (SAS) AF: 0.826 AC: 3966 AN: 4804

European-Finnish (FIN) AF: 0.629 AC: 6598 AN: 10494

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48718 AN: 67886

Other (OTH) AF: 0.761 AC: 1588 AN: 2086

Alfa AF: 0.735 Hom.: 161515

Bravo AF: 0.774

Asia WGS AF: 0.804 AC: 2798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.060
DANN	Benign	0.30
PhyloP100		-0.59
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: rs3131009; hg19: chr6-31098832;