6-31128024-G-A

Variant names:

• chr6-31128024-G-A
• rs9263715
• NM_014068.3:c.-64-1545G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014068.3(PSORS1C1):​c.-64-1545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,052 control chromosomes in the GnomAD database, including 4,859 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 0.24 (4859 hom., cov: 31)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 31 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	NM_014068.3	MANE Select	c.-64-1545G>A		intron	N/A	NP_054787.2	Q9UIG5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.-64-1545G>A		intron	N/A	ENSP00000259881.9	Q9UIG5-1
	PSORS1C1	ENST00000479581.5	TSL:1	n.62-11617G>A		intron	N/A
	PSORS1C1	ENST00000552747.1	TSL:1	n.54-10335G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36997 AN: 151934 Hom.: 4852 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.244 AC: 37026 AN: 152052 Hom.: 4859 Cov.: 31 AF XY: 0.247 AC XY: 18391 AN XY: 74352

African (AFR) AF: 0.307 AC: 12711 AN: 41450

American (AMR) AF: 0.214 AC: 3266 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1438 AN: 5158

South Asian (SAS) AF: 0.339 AC: 1636 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2183 AN: 10582

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13453 AN: 67978

Other (OTH) AF: 0.272 AC: 574 AN: 2108

Alfa AF: 0.216 Hom.: 11148

Bravo AF: 0.247

Asia WGS AF: 0.300 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.42
PhyloP100		-2.5
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: rs9263715; hg19: chr6-31095801;