rs2233945

Variant names:

• chr6-31139584-C-A
• rs2233945
• NM_014068.3:c.168-57C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31139584-C-A
• chr6-31139584-C-G
• chr6-31139584-C-T

Variant summary

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

The NM_014068.3(PSORS1C1):​c.168-57C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,564,258 control chromosomes in the GnomAD database, including 18,589 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 0.15 (1730 hom., cov: 31)
  • Exomes 𝑓: 0.15 (16859 hom.)
• Consequence: PSORS1C1 NM_014068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 30 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3	c.168-57C>A		intron_variant	Intron 5 of 5	ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10	c.168-57C>A		intron_variant	Intron 5 of 5	1	NM_014068.3	ENSP00000259881.9

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22129 AN: 152018 Hom.: 1722 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.151 AC: 212552 AN: 1412122 Hom.: 16859 Cov.: 29 AF XY: 0.148 AC XY: 103565 AN XY: 698566

African (AFR) AF: 0.160 AC: 5218 AN: 32560

American (AMR) AF: 0.102 AC: 4380 AN: 43130

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 2252 AN: 24430

East Asian (EAS) AF: 0.0460 AC: 1798 AN: 39064

South Asian (SAS) AF: 0.0766 AC: 6259 AN: 81686

European-Finnish (FIN) AF: 0.118 AC: 5600 AN: 47580

Middle Eastern (MID) AF: 0.146 AC: 633 AN: 4348

European-Non Finnish (NFE) AF: 0.165 AC: 178026 AN: 1080862

Other (OTH) AF: 0.143 AC: 8386 AN: 58462

GnomAD4 genome AF: 0.146 AC: 22175 AN: 152136 Hom.: 1730 Cov.: 31 AF XY: 0.142 AC XY: 10598 AN XY: 74382

African (AFR) AF: 0.160 AC: 6641 AN: 41488

American (AMR) AF: 0.133 AC: 2025 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 319 AN: 3468

East Asian (EAS) AF: 0.0726 AC: 376 AN: 5180

South Asian (SAS) AF: 0.0686 AC: 331 AN: 4828

European-Finnish (FIN) AF: 0.114 AC: 1212 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10777 AN: 67988

Other (OTH) AF: 0.160 AC: 337 AN: 2112

Alfa AF: 0.153 Hom.: 7236

Bravo AF: 0.147

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.88
PhyloP100		-0.17
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: rs2233945; hg19: chr6-31107361; COSMIC: COSV52535425; COSMIC: COSV52535425;