chr6-31139481-T-C

Variant names:

• chr6-31139481-T-C
• rs2285803
• NM_014068.3:c.168-160T>C

Variant summary

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

The NM_014068.3(PSORS1C1):​c.168-160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 666,548 control chromosomes in the GnomAD database, including 170,823 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 0.72 (39493 hom., cov: 31)
  • Exomes 𝑓: 0.71 (131330 hom.)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 51 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.168-160T>C		intron_variant	Intron 5 of 5	ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.168-160T>C		intron_variant	Intron 5 of 5	1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109544 AN: 151890 Hom.: 39458 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.750

GnomAD4 exome AF: 0.713 AC: 366853 AN: 514540 Hom.: 131330 Cov.: 6 AF XY: 0.711 AC XY: 190132 AN XY: 267412

African (AFR) AF: 0.743 AC: 10135 AN: 13648

American (AMR) AF: 0.742 AC: 14564 AN: 19632

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 10469 AN: 14308

East Asian (EAS) AF: 0.709 AC: 22238 AN: 31362

South Asian (SAS) AF: 0.705 AC: 33009 AN: 46812

European-Finnish (FIN) AF: 0.707 AC: 21245 AN: 30044

Middle Eastern (MID) AF: 0.774 AC: 1645 AN: 2124

European-Non Finnish (NFE) AF: 0.710 AC: 233226 AN: 328380

Other (OTH) AF: 0.720 AC: 20322 AN: 28230

GnomAD4 genome AF: 0.721 AC: 109632 AN: 152008 Hom.: 39493 Cov.: 31 AF XY: 0.722 AC XY: 53640 AN XY: 74286

African (AFR) AF: 0.747 AC: 30978 AN: 41460

American (AMR) AF: 0.739 AC: 11290 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2444 AN: 3466

East Asian (EAS) AF: 0.702 AC: 3628 AN: 5166

South Asian (SAS) AF: 0.686 AC: 3307 AN: 4822

European-Finnish (FIN) AF: 0.709 AC: 7491 AN: 10566

Middle Eastern (MID) AF: 0.776 AC: 225 AN: 290

European-Non Finnish (NFE) AF: 0.706 AC: 47983 AN: 67938

Other (OTH) AF: 0.748 AC: 1576 AN: 2108

Alfa AF: 0.711 Hom.: 108490

Bravo AF: 0.727

Asia WGS AF: 0.738 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		-0.48
PromoterAI		-0.0080	Neutral
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: rs2285803; hg19: chr6-31107258; COSMIC: COSV52536491; COSMIC: COSV52536491;