rs6917517

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 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.-536C>T		upstream_gene	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.-536C>T		upstream_gene	N/A	ENSP00000259881.9
	PSORS1C1	ENST00000479581.5	TSL:1	n.-247C>T		upstream_gene	N/A
	PSORS1C1	ENST00000467107.1	TSL:5	n.-166C>T		upstream_gene	N/A

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

African (AFR) AF: 0.102 AC: 4215 AN: 41520

American (AMR) AF: 0.201 AC: 3080 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1012 AN: 5160

South Asian (SAS) AF: 0.321 AC: 1546 AN: 4814

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10578

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11251 AN: 67996

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.173 Hom.: 9382

Bravo AF: 0.157

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.48
PhyloP100		0.55
PromoterAI		-0.034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6917517; hg19: chr6-31082361;