Genetic Variant PSORS1C1:c.168-57C>A (chr6-31139584-C-A) – 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.168-57C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,564,258 control chromosomes in the GnomAD database, including 18,589 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 0.15 ( 1730 hom., cov: 31)

Exomes 𝑓: 0.15 ( 16859 hom. )

Consequence

PSORS1C1
NM_014068.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Publications

30 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3 link	c.168-57C>A		intron_variant	Intron 5 of 5	ENST00000259881.10	NP_054787.2	Q9UIG5-1D2IYL0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C1	ENST00000259881.10 link	c.168-57C>A		intron_variant	Intron 5 of 5	1	NM_014068.3	ENSP00000259881.9		Q9UIG5-1

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22129

AN:

152018

Hom.:

1722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.0920

Gnomad EAS

AF:

0.0724

Gnomad SAS

AF:

0.0673

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.162

GnomAD4 exome

AF:

0.151

AC:

212552

AN:

1412122

Hom.:

16859

Cov.:

AF XY:

0.148

AC XY:

103565

AN XY:

698566

show subpopulations

African (AFR)

AF:

0.160

AC:

5218

AN:

32560

American (AMR)

AF:

0.102

AC:

4380

AN:

43130

Ashkenazi Jewish (ASJ)

AF:

0.0922

AC:

2252

AN:

24430

East Asian (EAS)

AF:

0.0460

AC:

1798

AN:

39064

South Asian (SAS)

AF:

0.0766

AC:

6259

AN:

81686

European-Finnish (FIN)

AF:

0.118

AC:

5600

AN:

47580

Middle Eastern (MID)

AF:

0.146

AC:

633

AN:

4348

European-Non Finnish (NFE)

AF:

0.165

AC:

178026

AN:

1080862

Other (OTH)

AF:

0.143

AC:

8386

AN:

58462

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

9163

18326

27490

36653

45816

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6346

12692

19038

25384

31730

<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:

0.146

AC:

22175

AN:

152136

Hom.:

1730

Cov.:

AF XY:

0.142

AC XY:

10598

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.160

AC:

6641

AN:

41488

American (AMR)

AF:

0.133

AC:

2025

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0920

AC:

319

AN:

3468

East Asian (EAS)

AF:

0.0726

AC:

376

AN:

5180

South Asian (SAS)

AF:

0.0686

AC:

331

AN:

4828

European-Finnish (FIN)

AF:

0.114

AC:

1212

AN:

10598

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10777

AN:

67988

Other (OTH)

AF:

0.160

AC:

337

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

943

1886

2830

3773

4716

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.153

Hom.:

7236

Bravo

AF:

0.147

Asia WGS

AF:

0.101

AC:

354

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.8

(source)

DANN

Benign

0.88

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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