Genetic Variant PSORS1C1:c.13+31T>G (chr6-31129676-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014068.3(PSORS1C1):c.13+31T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 779,170 control chromosomes in the GnomAD database, including 217,178 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 0.76 ( 44837 hom., cov: 32)

Exomes 𝑓: 0.74 ( 172341 hom. )

Consequence

PSORS1C1
NM_014068.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

20 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:

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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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014068.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	NM_014068.3	MANE Select	c.13+31T>G		intron	N/A	NP_054787.2	Q9UIG5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.13+31T>G	intron	N/A	ENSP00000259881.9	Q9UIG5-1
PSORS1C1	ENST00000479581.5	TSL:1	n.62-9965T>G	intron	N/A
PSORS1C1	ENST00000552747.1	TSL:1	n.54-8683T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.764

AC:

116084

AN:

151954

Hom.:

44801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.859

Gnomad AMI

AF:

0.664

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.817

Gnomad EAS

AF:

0.891

Gnomad SAS

AF:

0.825

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.764

GnomAD2 exomes

AF:

0.741

AC:

180887

AN:

244184

AF XY:

0.746

show subpopulations

Gnomad AFR exome

AF:

0.859

Gnomad AMR exome

AF:

0.650

Gnomad ASJ exome

AF:

0.815

Gnomad EAS exome

AF:

0.898

Gnomad FIN exome

AF:

0.629

Gnomad NFE exome

AF:

0.719

Gnomad OTH exome

AF:

0.753

GnomAD4 exome

AF:

0.737

AC:

462332

AN:

627098

Hom.:

172341

Cov.:

AF XY:

0.743

AC XY:

253892

AN XY:

341700

show subpopulations

African (AFR)

AF:

0.856

AC:

15140

AN:

17680

American (AMR)

AF:

0.663

AC:

28933

AN:

43670

Ashkenazi Jewish (ASJ)

AF:

0.813

AC:

17031

AN:

20958

East Asian (EAS)

AF:

0.874

AC:

31486

AN:

36034

South Asian (SAS)

AF:

0.822

AC:

57332

AN:

69730

European-Finnish (FIN)

AF:

0.633

AC:

32939

AN:

51996

Middle Eastern (MID)

AF:

0.809

AC:

3354

AN:

4148

European-Non Finnish (NFE)

AF:

0.718

AC:

251326

AN:

349816

Other (OTH)

AF:

0.750

AC:

24791

AN:

33066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

5806

11613

17419

23226

29032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1366

2732

4098

5464

6830

<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:

0.764

AC:

116173

AN:

152072

Hom.:

44837

Cov.:

AF XY:

0.762

AC XY:

56618

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.859

AC:

35643

AN:

41496

American (AMR)

AF:

0.736

AC:

11244

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.817

AC:

2836

AN:

3470

East Asian (EAS)

AF:

0.891

AC:

4611

AN:

5176

South Asian (SAS)

AF:

0.826

AC:

3984

AN:

4826

European-Finnish (FIN)

AF:

0.628

AC:

6631

AN:

10556

Middle Eastern (MID)

AF:

0.769

AC:

226

AN:

294

European-Non Finnish (NFE)

AF:

0.718

AC:

48786

AN:

67960

Other (OTH)

AF:

0.762

AC:

1608

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1363

2726

4089

5452

6815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

862

1724

2586

3448

4310

<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:

0.736

Hom.:

42498

Bravo

AF:

0.775

Asia WGS

AF:

0.812

AC:

2825

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.051

(source)

DANN

Benign

0.45

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over