rs9263827

Variant names:

• chr6-31181268-C-T
• rs9263827
• ENST00000412143.2:n.94-3369G>A

Variant summary

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

The ENST00000412143.2(PSORS1C3):​n.94-3369G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0885 in 137,996 control chromosomes in the GnomAD database, including 742 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 0.088 (742 hom., cov: 28)
• Consequence: PSORS1C3 ENST00000412143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 6 publications found

Genes affected

PSORS1C3 (HGNC:17203): (psoriasis susceptibility 1 candidate 3)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt
PSORS1C3	NR_026816.2	n.293-3369G>A		intron_variant	Intron 1 of 3
PSORS1C3	NR_152828.1	n.293-3369G>A		intron_variant	Intron 1 of 4
PSORS1C3	NR_152829.1	n.293-3369G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C3	ENST00000412143.2	n.94-3369G>A		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 12172 AN: 137888 Hom.: 737 Cov.: 28

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0157

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.0842

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0885 AC: 12207 AN: 137996 Hom.: 742 Cov.: 28 AF XY: 0.0876 AC XY: 5871 AN XY: 67008

African (AFR) AF: 0.174 AC: 6462 AN: 37104

American (AMR) AF: 0.0867 AC: 1188 AN: 13702

Ashkenazi Jewish (ASJ) AF: 0.0747 AC: 249 AN: 3332

East Asian (EAS) AF: 0.0843 AC: 363 AN: 4304

South Asian (SAS) AF: 0.0577 AC: 236 AN: 4088

European-Finnish (FIN) AF: 0.0104 AC: 91 AN: 8732

Middle Eastern (MID) AF: 0.101 AC: 16 AN: 158

European-Non Finnish (NFE) AF: 0.0530 AC: 3385 AN: 63872

Other (OTH) AF: 0.109 AC: 204 AN: 1876

Alfa AF: 0.0660 Hom.: 314

Bravo AF: 0.0906

Asia WGS AF: 0.0680 AC: 235 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	5.5
DANN	Benign	0.74
PhyloP100		0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9263827; hg19: chr6-31149045;