rs3130558

Variant names:

• chr6-31129406-C-G
• rs3130558
• NM_014068.3:c.-64-163C>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-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 rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.-64-163C>G		intron_variant	Intron 2 of 5	ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-64-163C>G		intron_variant	Intron 2 of 5	1	NM_014068.3	ENSP00000259881.9

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

African (AFR) AF: 0.861 AC: 35742 AN: 41528

American (AMR) AF: 0.741 AC: 11319 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4604 AN: 5168

South Asian (SAS) AF: 0.827 AC: 3983 AN: 4818

European-Finnish (FIN) AF: 0.629 AC: 6639 AN: 10562

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49434 AN: 67970

Other (OTH) AF: 0.768 AC: 1621 AN: 2112

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
PhyloP100		0.42
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: rs3130558; hg19: chr6-31097183;