rs6917517

Variant names:

• chr6-31114584-C-T
• rs6917517
• NM_014068.3:c.-536C>T

Variant summary

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

The NM_014068.3(PSORS1C1):​c.-536C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,150 control chromosomes in the GnomAD database, including 2,251 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 0.16 (2251 hom., cov: 31)
• Consequence: PSORS1C1 NM_014068.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.-536C>T		upstream_gene_variant		ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-536C>T		upstream_gene_variant		1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24618 AN: 152034 Hom.: 2255 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.162 AC: 24609 AN: 152150 Hom.: 2251 Cov.: 31 AF XY: 0.168 AC XY: 12510 AN XY: 74362

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.183

Alfa AF: 0.159 Hom.: 185

Bravo AF: 0.157

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6917517; hg19: chr6-31082361;