Genetic Variant PSORS1C1:n.186A>G (chr6-31138491-A-G) – 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.186A>G 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 0.343 in 1,609,828 control chromosomes in the GnomAD database, including 96,815 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 0.37 ( 10630 hom., cov: 29)

Exomes 𝑓: 0.34 ( 86185 hom. )

Consequence

PSORS1C1
ENST00000552747.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Publications

74 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3 link	c.43+32A>G		intron_variant	Intron 4 of 5	ENST00000259881.10	NP_054787.2
PSORS1C2	NM_014069.3 link	c.56-185T>C		intron_variant	Intron 1 of 1	ENST00000259845.5	NP_054788.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10 link	c.43+32A>G		intron_variant	Intron 4 of 5	1	NM_014068.3	ENSP00000259881.9
PSORS1C2	ENST00000259845.5 link	c.56-185T>C		intron_variant	Intron 1 of 1	1	NM_014069.3	ENSP00000259845.4

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56063

AN:

151572

Hom.:

10615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.377

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.368

GnomAD2 exomes

AF:

0.329

AC:

81164

AN:

246496

AF XY:

0.330

show subpopulations

Gnomad AFR exome

AF:

0.450

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.371

Gnomad EAS exome

AF:

0.188

Gnomad FIN exome

AF:

0.363

Gnomad NFE exome

AF:

0.346

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.340

AC:

495315

AN:

1458136

Hom.:

86185

Cov.:

AF XY:

0.340

AC XY:

246487

AN XY:

725540

show subpopulations

African (AFR)

AF:

0.455

AC:

15220

AN:

33430

American (AMR)

AF:

0.294

AC:

13160

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.376

AC:

9815

AN:

26120

East Asian (EAS)

AF:

0.173

AC:

6879

AN:

39696

South Asian (SAS)

AF:

0.308

AC:

26524

AN:

86208

European-Finnish (FIN)

AF:

0.365

AC:

19068

AN:

52306

Middle Eastern (MID)

AF:

0.330

AC:

1902

AN:

5762

European-Non Finnish (NFE)

AF:

0.344

AC:

381733

AN:

1109622

Other (OTH)

AF:

0.349

AC:

21014

AN:

60278

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

16727

33454

50181

66908

83635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12140

24280

36420

48560

60700

<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:

0.370

AC:

56126

AN:

151692

Hom.:

10630

Cov.:

AF XY:

0.368

AC XY:

27260

AN XY:

74102

show subpopulations

African (AFR)

AF:

0.450

AC:

18575

AN:

41302

American (AMR)

AF:

0.301

AC:

4597

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1243

AN:

3470

East Asian (EAS)

AF:

0.199

AC:

1022

AN:

5144

South Asian (SAS)

AF:

0.337

AC:

1612

AN:

4782

European-Finnish (FIN)

AF:

0.377

AC:

3982

AN:

10552

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.349

AC:

23721

AN:

67874

Other (OTH)

AF:

0.365

AC:

771

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1730

3460

5191

6921

8651

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.351

Hom.:

42465

Bravo

AF:

0.368

Asia WGS

AF:

0.251

AC:

878

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.5

(source)

DANN

Benign

0.56

PhyloP100

0.083

PromoterAI

-0.0021

Neutral

(source)

Mutation Taster

=99/1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over