rs2233945

Positions:

• chr6-31139584-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014068.3(PSORS1C1):​c.168-57C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,564,258 control chromosomes in the GnomAD database, including 18,589 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 0.15 (1730 hom., cov: 31)
  • Exomes 𝑓: 0.15 (16859 hom.)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.168-57C>A		intron_variant		ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.168-57C>A		intron_variant		1	NM_014068.3	ENSP00000259881	P2
PSORS1C1	ENST00000479581.5	n.62-57C>A		intron_variant, non_coding_transcript_variant		1
PSORS1C1	ENST00000481450.2	c.-22-57C>A		intron_variant		2		ENSP00000447158
PSORS1C1	ENST00000547221.1	c.24-57C>A		intron_variant		3		ENSP00000449471	A2

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22129 AN: 152018 Hom.: 1722 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.151 AC: 212552 AN: 1412122 Hom.: 16859 Cov.: 29 AF XY: 0.148 AC XY: 103565 AN XY: 698566

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.102

Gnomad4 ASJ exome AF: 0.0922

Gnomad4 EAS exome AF: 0.0460

Gnomad4 SAS exome AF: 0.0766

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.165

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.146 AC: 22175 AN: 152136 Hom.: 1730 Cov.: 31 AF XY: 0.142 AC XY: 10598 AN XY: 74382

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.160

Alfa AF: 0.159 Hom.: 2945

Bravo AF: 0.147

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233945; hg19: chr6-31107361; COSMIC: COSV52535425; COSMIC: COSV52535425;