Genetic Variant PSORS1C1:n.1005T>C (chr6-31139310-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000552747.1(PSORS1C1):n.1005T>C variant causes a non coding transcript exon 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
ENST00000552747.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126

Publications

55 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3 link	c.168-331T>C		intron_variant	Intron 5 of 5	ENST00000259881.10	NP_054787.2
PSORS1C2	NM_014069.3 link	c.-284A>G		upstream_gene_variant		ENST00000259845.5	NP_054788.2

Ensembl

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

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

African (AFR)

AF:

0.743

AC:

9075

AN:

12212

American (AMR)

AF:

0.746

AC:

13283

AN:

17796

Ashkenazi Jewish (ASJ)

AF:

0.732

AC:

9848

AN:

13448

East Asian (EAS)

AF:

0.710

AC:

21732

AN:

30616

South Asian (SAS)

AF:

0.708

AC:

28878

AN:

40794

European-Finnish (FIN)

AF:

0.708

AC:

20676

AN:

29218

Middle Eastern (MID)

AF:

0.777

AC:

1487

AN:

1914

European-Non Finnish (NFE)

AF:

0.705

AC:

182585

AN:

259118

Other (OTH)

AF:

0.720

AC:

18188

AN:

25266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

4408

8815

13223

17630

22038

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

830

1660

2490

3320

4150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.722

AC:

109732

AN:

152006

Hom.:

39573

Cov.:

AF XY:

0.723

AC XY:

53704

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.750

AC:

31078

AN:

41444

American (AMR)

AF:

0.739

AC:

11282

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.706

AC:

2447

AN:

3468

East Asian (EAS)

AF:

0.702

AC:

3610

AN:

5144

South Asian (SAS)

AF:

0.687

AC:

3307

AN:

4816

European-Finnish (FIN)

AF:

0.709

AC:

7495

AN:

10572

Middle Eastern (MID)

AF:

0.779

AC:

229

AN:

294

European-Non Finnish (NFE)

AF:

0.706

AC:

47997

AN:

67976

Other (OTH)

AF:

0.747

AC:

1576

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1580

3160

4740

6320

7900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.714

Hom.:

160501

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

(source)

DANN

Benign

0.83

PhyloP100

0.13

PromoterAI

-0.0063

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over