Variant rs3094663 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014068.3(PSORS1C1):c.168-331T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 582,388 control chromosomes in the GnomAD database, including 148,791 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 0.72 ( 39573 hom., cov: 31)

Exomes 𝑓: 0.71 ( 109218 hom. )

Consequence

PSORS1C1
NM_014068.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C1	NM_014068.3 linkuse as main transcript	c.168-331T>C		intron_variant		ENST00000259881.10	NP_054787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10 linkuse as main transcript	c.168-331T>C		intron_variant		1	NM_014068.3	ENSP00000259881	P2	Q9UIG5-1

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

109644

AN:

151888

Hom.:

39538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.750

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.739

Gnomad ASJ

AF:

0.706

Gnomad EAS

AF:

0.701

Gnomad SAS

AF:

0.687

Gnomad FIN

AF:

0.709

Gnomad MID

AF:

0.785

Gnomad NFE

AF:

0.706

Gnomad OTH

AF:

0.749

GnomAD4 exome

AF:

0.710

AC:

305752

AN:

430382

Hom.:

109218

Cov.:

AF XY:

0.709

AC XY:

159470

AN XY:

225032

show subpopulations

Gnomad4 AFR exome

AF:

0.743

Gnomad4 AMR exome

AF:

0.746

Gnomad4 ASJ exome

AF:

0.732

Gnomad4 EAS exome

AF:

0.710

Gnomad4 SAS exome

AF:

0.708

Gnomad4 FIN exome

AF:

0.708

Gnomad4 NFE exome

AF:

0.705

Gnomad4 OTH exome

AF:

0.720

GnomAD4 genome

AF:

0.722

AC:

109732

AN:

152006

Hom.:

39573

Cov.:

AF XY:

0.723

AC XY:

53704

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.750

Gnomad4 AMR

AF:

0.739

Gnomad4 ASJ

AF:

0.706

Gnomad4 EAS

AF:

0.702

Gnomad4 SAS

AF:

0.687

Gnomad4 FIN

AF:

0.709

Gnomad4 NFE

AF:

0.706

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.714

Hom.:

72704

Bravo

AF:

0.727

Asia WGS

AF:

0.738

AC:

2566

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.4

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over