rs6929464

Variant names:

• chr6-31130141-T-C
• rs6929464
• NM_014068.3:c.13+496T>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.13+496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 128,330 control chromosomes in the GnomAD database, including 1,278 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 0.14 (1278 hom., cov: 29)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 18 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.13+496T>C		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+496T>C		intron_variant	Intron 3 of 5	1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.144 AC: 18522 AN: 128220 Hom.: 1270 Cov.: 29

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.145 AC: 18557 AN: 128330 Hom.: 1278 Cov.: 29 AF XY: 0.144 AC XY: 9056 AN XY: 62714

African (AFR) AF: 0.234 AC: 7348 AN: 31416

American (AMR) AF: 0.101 AC: 1302 AN: 12892

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 569 AN: 3192

East Asian (EAS) AF: 0.0719 AC: 288 AN: 4008

South Asian (SAS) AF: 0.211 AC: 896 AN: 4242

European-Finnish (FIN) AF: 0.0748 AC: 692 AN: 9250

Middle Eastern (MID) AF: 0.280 AC: 70 AN: 250

European-Non Finnish (NFE) AF: 0.115 AC: 6928 AN: 60438

Other (OTH) AF: 0.159 AC: 279 AN: 1750

Alfa AF: 0.178 Hom.: 6388

Bravo AF: 0.125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.53
PhyloP100		-0.37
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: rs6929464; hg19: chr6-31097918;