rs6909321

chr6-31125413-G-Achr6-31125413-G-T

Variant summary

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

The NM_014068.3(PSORS1C1):c.-228-263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,132 control chromosomes in the GnomAD database, including 1,317 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 0.13 (1317 hom., cov: 32)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSORS1C1	NM_014068.3	c.-228-263G>A		intron_variant		ENST00000259881.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-228-263G>A		intron_variant		1	NM_014068.3	P2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19181 AN: 152014 Hom.: 1314 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.126 AC: 19203 AN: 152132 Hom.: 1317 Cov.: 32 AF XY: 0.126 AC XY: 9400 AN XY: 74370

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.130

Alfa AF: 0.105 Hom.: 1310

Bravo AF: 0.129

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.2
Dann	Benign	0.62

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: rs6909321; hg19: chr6-31093190;