dbSNP rs1265095: PSORS1C1:n.561G>A (chr6-31138866-G-A) – 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.561G>A 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 0.538 in 1,600,658 control chromosomes in the GnomAD database, including 236,555 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 0.59 ( 26627 hom., cov: 31)

Exomes 𝑓: 0.53 ( 209928 hom. )

Consequence

PSORS1C1
ENST00000552747.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16

Publications

21 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C1	NM_014068.3 link	c.167+87G>A		intron_variant	Intron 5 of 5	ENST00000259881.10	NP_054787.2
PSORS1C2	NM_014069.3 link	c.55+106C>T		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.167+87G>A		intron_variant	Intron 5 of 5	1	NM_014068.3	ENSP00000259881.9
PSORS1C2	ENST00000259845.5 link	c.55+106C>T		intron_variant	Intron 1 of 1	1	NM_014069.3	ENSP00000259845.4

Frequencies

GnomAD3 genomes

AF:

0.586

AC:

89010

AN:

151804

Hom.:

26592

Cov.:

show subpopulations

Gnomad AFR

AF:

0.694

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.798

Gnomad EAS

AF:

0.455

Gnomad SAS

AF:

0.712

Gnomad FIN

AF:

0.563

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.522

Gnomad OTH

AF:

0.598

GnomAD4 exome

AF:

0.533

AC:

771494

AN:

1448736

Hom.:

209928

Cov.:

AF XY:

0.539

AC XY:

388730

AN XY:

720664

show subpopulations

African (AFR)

AF:

0.699

AC:

23240

AN:

33264

American (AMR)

AF:

0.519

AC:

23118

AN:

44584

Ashkenazi Jewish (ASJ)

AF:

0.793

AC:

20481

AN:

25830

East Asian (EAS)

AF:

0.469

AC:

18553

AN:

39582

South Asian (SAS)

AF:

0.688

AC:

59098

AN:

85878

European-Finnish (FIN)

AF:

0.549

AC:

29194

AN:

53192

Middle Eastern (MID)

AF:

0.627

AC:

3588

AN:

5724

European-Non Finnish (NFE)

AF:

0.509

AC:

560061

AN:

1100748

Other (OTH)

AF:

0.570

AC:

34161

AN:

59934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

19286

38571

57857

77142

96428

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16198

32396

48594

64792

80990

<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:

0.586

AC:

89086

AN:

151922

Hom.:

26627

Cov.:

AF XY:

0.588

AC XY:

43679

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.694

AC:

28748

AN:

41410

American (AMR)

AF:

0.547

AC:

8353

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.798

AC:

2772

AN:

3472

East Asian (EAS)

AF:

0.455

AC:

2344

AN:

5150

South Asian (SAS)

AF:

0.711

AC:

3425

AN:

4816

European-Finnish (FIN)

AF:

0.563

AC:

5945

AN:

10556

Middle Eastern (MID)

AF:

0.673

AC:

198

AN:

294

European-Non Finnish (NFE)

AF:

0.522

AC:

35470

AN:

67932

Other (OTH)

AF:

0.596

AC:

1255

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1905

3810

5716

7621

9526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.563

Hom.:

25387

Bravo

AF:

0.589

Asia WGS

AF:

0.589

AC:

2052

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.3

(source)

DANN

Benign

0.64

PhyloP100

1.2

PromoterAI

-0.037

Neutral

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over