Genetic Variant NM_014069.3:c.*95G>A (chr6-31137856-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014069.3(PSORS1C2):c.*95G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 558,006 control chromosomes in the GnomAD database, including 189,542 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 0.84 ( 53876 hom., cov: 31)

Exomes 𝑓: 0.82 ( 135666 hom. )

Consequence

PSORS1C2
NM_014069.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.11

Publications

31 publications found

Variant links:

Genes affected

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:

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:

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSORS1C2	NM_014069.3 link	c.*95G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000259845.5	NP_054788.2	Q9UIG4A0A1U9X9A6
PSORS1C1	NM_014068.3 link	c.14-574C>T		intron_variant	Intron 3 of 5	ENST00000259881.10	NP_054787.2	Q9UIG5-1D2IYL0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C2	ENST00000259845.5 link	c.*95G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_014069.3	ENSP00000259845.4		Q9UIG4
PSORS1C1	ENST00000259881.10 link	c.14-574C>T		intron_variant	Intron 3 of 5	1	NM_014068.3	ENSP00000259881.9		Q9UIG5-1

Frequencies

GnomAD3 genomes

AF:

0.840

AC:

127782

AN:

152082

Hom.:

53828

Cov.:

show subpopulations

Gnomad AFR

AF:

0.884

Gnomad AMI

AF:

0.947

Gnomad AMR

AF:

0.855

Gnomad ASJ

AF:

0.939

Gnomad EAS

AF:

0.760

Gnomad SAS

AF:

0.813

Gnomad FIN

AF:

0.807

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.816

Gnomad OTH

AF:

0.853

GnomAD4 exome

AF:

0.816

AC:

331273

AN:

405806

Hom.:

135666

Cov.:

AF XY:

0.816

AC XY:

169405

AN XY:

207630

show subpopulations

African (AFR)

AF:

0.892

AC:

9121

AN:

10220

American (AMR)

AF:

0.845

AC:

9971

AN:

11804

Ashkenazi Jewish (ASJ)

AF:

0.942

AC:

10847

AN:

11510

East Asian (EAS)

AF:

0.775

AC:

20303

AN:

26192

South Asian (SAS)

AF:

0.801

AC:

19111

AN:

23858

European-Finnish (FIN)

AF:

0.799

AC:

31295

AN:

39154

Middle Eastern (MID)

AF:

0.858

AC:

1505

AN:

1754

European-Non Finnish (NFE)

AF:

0.813

AC:

210261

AN:

258598

Other (OTH)

AF:

0.830

AC:

18859

AN:

22716

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3596

7191

10787

14382

17978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1848

3696

5544

7392

9240

<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:

0.840

AC:

127894

AN:

152200

Hom.:

53876

Cov.:

AF XY:

0.839

AC XY:

62440

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.884

AC:

36712

AN:

41542

American (AMR)

AF:

0.856

AC:

13086

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.939

AC:

3260

AN:

3472

East Asian (EAS)

AF:

0.760

AC:

3925

AN:

5164

South Asian (SAS)

AF:

0.814

AC:

3925

AN:

4824

European-Finnish (FIN)

AF:

0.807

AC:

8546

AN:

10588

Middle Eastern (MID)

AF:

0.884

AC:

260

AN:

294

European-Non Finnish (NFE)

AF:

0.816

AC:

55513

AN:

68000

Other (OTH)

AF:

0.854

AC:

1805

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1050

2101

3151

4202

5252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.827

Hom.:

213351

Bravo

AF:

0.845

Asia WGS

AF:

0.800

AC:

2781

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.21

(source)

DANN

Benign

0.73

PhyloP100

-3.1

PromoterAI

-0.030

Neutral

(source)

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