chr6-31133165-G-A

Variant names:

• chr6-31133165-G-A
• rs3823418
• NM_014068.3:c.13+3520G>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+3520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,870 control chromosomes in the GnomAD database, including 4,671 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 0.23 (4671 hom., cov: 30)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 34 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.13+3520G>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+3520G>A		intron_variant	Intron 3 of 5	1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34520 AN: 151752 Hom.: 4653 Cov.: 30

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.228 AC: 34572 AN: 151870 Hom.: 4671 Cov.: 30 AF XY: 0.228 AC XY: 16890 AN XY: 74238

African (AFR) AF: 0.372 AC: 15381 AN: 41358

American (AMR) AF: 0.179 AC: 2724 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.180 AC: 927 AN: 5160

South Asian (SAS) AF: 0.263 AC: 1261 AN: 4800

European-Finnish (FIN) AF: 0.134 AC: 1411 AN: 10558

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11334 AN: 67972

Other (OTH) AF: 0.243 AC: 510 AN: 2100

Alfa AF: 0.185 Hom.: 12500

Bravo AF: 0.238

Asia WGS AF: 0.221 AC: 771 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.61
PhyloP100		-0.98
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: rs3823418; hg19: chr6-31100942;