6-31125810-G-A

Position:

• chr6-31125810-G-A

Variant summary

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

The NM_014068.3(PSORS1C1):​c.-94G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,184 control chromosomes in the GnomAD database, including 5,120 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 0.25 (5117 hom., cov: 33)
  • Exomes 𝑓: 0.36 (3 hom.)
• Consequence: PSORS1C1 NM_014068.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.-94G>A		5_prime_UTR_variant	2/6	ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-94G>A		5_prime_UTR_variant	2/6	1	NM_014068.3	ENSP00000259881	P2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37805 AN: 152030 Hom.: 5113 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.277

GnomAD4 exome AF: 0.361 AC: 13 AN: 36 Hom.: 3 Cov.: 0 AF XY: 0.367 AC XY: 11 AN XY: 30

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.350

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.249 AC: 37830 AN: 152148 Hom.: 5117 Cov.: 33 AF XY: 0.252 AC XY: 18768 AN XY: 74398

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.275

Alfa AF: 0.226 Hom.: 6726

Bravo AF: 0.253

Asia WGS AF: 0.286 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3815087; hg19: chr6-31093587;