Genetic Variant PSORS1C3:n.93+3578A>T (chr6-31182448-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000412143.2(PSORS1C3):n.93+3578A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 152,320 control chromosomes in the GnomAD database, including 220 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 0.043 ( 220 hom., cov: 31)

Consequence

PSORS1C3
ENST00000412143.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

2 publications found

Variant links:

Genes affected

PSORS1C3 (HGNC:17203): (psoriasis susceptibility 1 candidate 3)

PSORS1C3 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
PSORS1C3	NR_026816.2 link	n.292+3578A>T	intron_variant	Intron 1 of 3
PSORS1C3	NR_152828.1 link	n.292+3578A>T	intron_variant	Intron 1 of 4
PSORS1C3	NR_152829.1 link	n.292+3578A>T	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSORS1C3	ENST00000412143.2 link	n.93+3578A>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.0428

AC:

6510

AN:

152202

Hom.:

219

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0161

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0590

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.0133

Gnomad SAS

AF:

0.0876

Gnomad FIN

AF:

0.0392

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0457

Gnomad OTH

AF:

0.0561

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0427

AC:

6507

AN:

152320

Hom.:

220

Cov.:

AF XY:

0.0440

AC XY:

3276

AN XY:

74484

show subpopulations

African (AFR)

AF:

0.0160

AC:

667

AN:

41572

American (AMR)

AF:

0.0588

AC:

900

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

750

AN:

3470

East Asian (EAS)

AF:

0.0135

AC:

AN:

5194

South Asian (SAS)

AF:

0.0870

AC:

420

AN:

4826

European-Finnish (FIN)

AF:

0.0392

AC:

416

AN:

10614

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0457

AC:

3108

AN:

68030

Other (OTH)

AF:

0.0570

AC:

120

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

325

651

976

1302

1627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<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:

0.0497

Hom.:

Bravo

AF:

0.0429

Asia WGS

AF:

0.0550

AC:

191

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.0

(source)

DANN

Benign

0.45

PhyloP100

0.055

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over