rs1265098

Variant names:

• chr6-31138400-T-A
• rs1265098
• ENST00000552747.1:n.95T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31138400-T-A
• chr6-31138400-T-C
• chr6-31138400-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000552747.1(PSORS1C1):​n.95T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,460,188 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 27)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: PSORS1C1 ENST00000552747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 35 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]

PSORS1C2 (HGNC:17199): (psoriasis susceptibility 1 candidate 2) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.14-30T>A		intron_variant	Intron 3 of 5	ENST00000259881.10	NP_054787.2
PSORS1C2	NM_014069.3	c.56-94A>T		intron_variant	Intron 1 of 1	ENST00000259845.5	NP_054788.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.14-30T>A		intron_variant	Intron 3 of 5	1	NM_014068.3	ENSP00000259881.9
PSORS1C2	ENST00000259845.5	c.56-94A>T		intron_variant	Intron 1 of 1	1	NM_014069.3	ENSP00000259845.4

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.00000479 AC: 7 AN: 1460188 Hom.: 0 Cov.: 39 AF XY: 0.00000688 AC XY: 5 AN XY: 726458

African (AFR) AF: 0.00 AC: 0 AN: 33472

American (AMR) AF: 0.00 AC: 0 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.00 AC: 0 AN: 86252

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52310

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00000630 AC: 7 AN: 1111486

Other (OTH) AF: 0.00 AC: 0 AN: 60362

GnomAD4 genome Cov.: 27

Alfa AF: 0.00 Hom.: 6478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.49
PhyloP100		0.32
PromoterAI		0.11	Neutral

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: rs1265098; hg19: chr6-31106177;