dbSNP rs3094663: PSORS1C1:n.1005T>A (chr6-31139310-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000552747.1(PSORS1C1):n.1005T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PSORS1C1
ENST00000552747.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126

Publications

0 publications found

Variant links:

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 links:

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

PSORS1C2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3 link	c.168-331T>A		intron_variant	Intron 5 of 5	ENST00000259881.10	NP_054787.2	Q9UIG5-1D2IYL0
PSORS1C2	NM_014069.3 link	c.-284A>T		upstream_gene_variant		ENST00000259845.5	NP_054788.2	Q9UIG4A0A1U9X9A6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10 link	c.168-331T>A		intron_variant	Intron 5 of 5	1	NM_014068.3	ENSP00000259881.9		Q9UIG5-1
PSORS1C2	ENST00000259845.5 link	c.-284A>T		upstream_gene_variant		1	NM_014069.3	ENSP00000259845.4		Q9UIG4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

430668

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

225188

African (AFR)

AF:

0.00

AC:

AN:

12212

American (AMR)

AF:

0.00

AC:

AN:

17806

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13450

East Asian (EAS)

AF:

0.00

AC:

AN:

30630

South Asian (SAS)

AF:

0.00

AC:

AN:

40828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29252

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1914

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

259296

Other (OTH)

AF:

0.00

AC:

AN:

25280

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.7

(source)

DANN

Benign

0.89

PhyloP100

0.13

PromoterAI

-0.12

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over