Variant rs2285803 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.168-160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 666,548 control chromosomes in the GnomAD database, including 170,823 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 ( 39493 hom., cov: 31)

Exomes 𝑓: 0.71 ( 131330 hom. )

Consequence

PSORS1C1
NM_014068.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.480

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:

PSORS1C1 (HGNC:):

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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.168-160T>C		intron_variant		ENST00000259881.10	NP_054787.2	Q9UIG5-1D2IYL0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10 linkuse as main transcript	c.168-160T>C		intron_variant		1	NM_014068.3	ENSP00000259881.9		Q9UIG5-1

Frequencies

GnomAD3 genomes

AF:

0.721

AC:

109544

AN:

151890

Hom.:

39458

Cov.:

show subpopulations

Gnomad AFR

AF:

0.747

Gnomad AMI

AF:

0.782

Gnomad AMR

AF:

0.739

Gnomad ASJ

AF:

0.705

Gnomad EAS

AF:

0.702

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.709

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.706

Gnomad OTH

AF:

0.750

GnomAD4 exome

AF:

0.713

AC:

366853

AN:

514540

Hom.:

131330

Cov.:

AF XY:

0.711

AC XY:

190132

AN XY:

267412

show subpopulations

Gnomad4 AFR exome

AF:

0.743

Gnomad4 AMR exome

AF:

0.742

Gnomad4 ASJ exome

AF:

0.732

Gnomad4 EAS exome

AF:

0.709

Gnomad4 SAS exome

AF:

0.705

Gnomad4 FIN exome

AF:

0.707

Gnomad4 NFE exome

AF:

0.710

Gnomad4 OTH exome

AF:

0.720

GnomAD4 genome

AF:

0.721

AC:

109632

AN:

152008

Hom.:

39493

Cov.:

AF XY:

0.722

AC XY:

53640

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.747

Gnomad4 AMR

AF:

0.739

Gnomad4 ASJ

AF:

0.705

Gnomad4 EAS

AF:

0.702

Gnomad4 SAS

AF:

0.686

Gnomad4 FIN

AF:

0.709

Gnomad4 NFE

AF:

0.706

Gnomad4 OTH

AF:

0.748

Alfa

AF:

0.714

Hom.:

32543

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

-0.88

CADD

Benign

4.5

DANN

Benign

0.75

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

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