6-31125550-A-G

Position:

• chr6-31125550-A-G

Variant summary

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

The NM_014068.3(PSORS1C1):​c.-228-126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,876 control chromosomes in the GnomAD database, including 19,054 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 0.49 (19054 hom., cov: 32)
  • Exomes 𝑓: 0.41 (11 hom.)
  • Failed GnomAD Quality Control
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

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]

PSORS1C1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.-228-126A>G		intron_variant		ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-228-126A>G		intron_variant		1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74766 AN: 151758 Hom.: 19036 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.516

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.407 AC: 48 AN: 118 Hom.: 11 AF XY: 0.372 AC XY: 32 AN XY: 86

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.382

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.493 AC: 74831 AN: 151876 Hom.: 19054 Cov.: 32 AF XY: 0.493 AC XY: 36629 AN XY: 74228

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.516

Alfa AF: 0.465 Hom.: 2360

Bravo AF: 0.511

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.41

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: rs3094198; hg19: chr6-31093327;