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.

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.168-57C>A		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.168-57C>A	intron	N/A	ENSP00000259881.9	Q9UIG5-1
PSORS1C1	ENST00000479581.5	TSL:1	n.62-57C>A	intron	N/A
PSORS1C1	ENST00000547221.1	TSL:3	c.24-57C>A	intron	N/A	ENSP00000449471.1	A0A0C4DGJ2

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over