rs3095307

Variant names:

• chr6-31124272-G-C
• rs3095307
• NM_014068.3:c.-228-1404G>C

Variant summary

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

The NM_014068.3(PSORS1C1):​c.-228-1404G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,910 control chromosomes in the GnomAD database, including 26,415 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 0.58 (26415 hom., cov: 30)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 17 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.-228-1404G>C		intron_variant	Intron 1 of 5	ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.-228-1404G>C		intron_variant	Intron 1 of 5	1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87673 AN: 151792 Hom.: 26395 Cov.: 30

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.578 AC: 87742 AN: 151910 Hom.: 26415 Cov.: 30 AF XY: 0.574 AC XY: 42612 AN XY: 74222

African (AFR) AF: 0.751 AC: 31110 AN: 41400

American (AMR) AF: 0.577 AC: 8808 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3208 AN: 5156

South Asian (SAS) AF: 0.430 AC: 2073 AN: 4816

European-Finnish (FIN) AF: 0.456 AC: 4807 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33597 AN: 67948

Other (OTH) AF: 0.594 AC: 1251 AN: 2106

Alfa AF: 0.534 Hom.: 3107

Bravo AF: 0.599

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		-0.23
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: rs3095307; hg19: chr6-31092049;