6-31131984-G-A

Variant names:

• chr6-31131984-G-A
• rs12525170
• NM_014068.3:c.13+2339G>A

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+2339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,230 control chromosomes in the GnomAD database, including 405 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 0.065 (405 hom., cov: 33)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014068.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	NM_014068.3	MANE Select	c.13+2339G>A		intron	N/A	NP_054787.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.13+2339G>A		intron	N/A	ENSP00000259881.9
	PSORS1C1	ENST00000479581.5	TSL:1	n.62-7657G>A		intron	N/A
	PSORS1C1	ENST00000552747.1	TSL:1	n.54-6375G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0653 AC: 9927 AN: 152110 Hom.: 409 Cov.: 33

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0651 AC: 9913 AN: 152230 Hom.: 405 Cov.: 33 AF XY: 0.0690 AC XY: 5133 AN XY: 74428

African (AFR) AF: 0.0237 AC: 983 AN: 41536

American (AMR) AF: 0.0822 AC: 1257 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3468

East Asian (EAS) AF: 0.130 AC: 674 AN: 5184

South Asian (SAS) AF: 0.182 AC: 878 AN: 4822

European-Finnish (FIN) AF: 0.0891 AC: 945 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0717 AC: 4875 AN: 68010

Other (OTH) AF: 0.0626 AC: 132 AN: 2108

Alfa AF: 0.0627 Hom.: 48

Bravo AF: 0.0601

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		-0.74
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: rs12525170; hg19: chr6-31099761;