Variant chr6-31115952-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001264.5(CDSN):c.*73T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,354,914 control chromosomes in the GnomAD database, including 78,602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 13517 hom., cov: 32)

Exomes 𝑓: 0.32 ( 65085 hom. )

Consequence

CDSN
NM_001264.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.157

Variant links:

Genes affected

CDSN (HGNC:1802): (corneodesmosin) This gene encodes a protein found in corneodesmosomes, which localize to human epidermis and other cornified squamous epithelia. The encoded protein undergoes a series of cleavages during corneocyte maturation. This gene is highly polymorphic in human populations, and variation has been associated with skin diseases such as psoriasis, hypotrichosis and peeling skin syndrome. The gene is located in the major histocompatibility complex (MHC) class I region on chromosome 6. [provided by RefSeq, Dec 2014]

CDSN 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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 6-31115952-A-C is Benign according to our data. Variant chr6-31115952-A-C is described in ClinVar as [Benign]. Clinvar id is 1230203.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDSN	NM_001264.5 linkuse as main transcript	c.*73T>G		3_prime_UTR_variant	2/2	ENST00000376288.3
PSORS1C1	NM_014068.3 linkuse as main transcript	c.-229+1061A>C		intron_variant		ENST00000259881.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDSN	ENST00000376288.3 linkuse as main transcript	c.*73T>G		3_prime_UTR_variant	2/2	1	NM_001264.5	P1
PSORS1C1	ENST00000259881.10 linkuse as main transcript	c.-229+1061A>C		intron_variant		1	NM_014068.3	P2	Q9UIG5-1

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62017

AN:

151756

Hom.:

13502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.410

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.411

GnomAD4 exome

AF:

0.322

AC:

386957

AN:

1203040

Hom.:

65085

Cov.:

AF XY:

0.321

AC XY:

194722

AN XY:

607060

show subpopulations

Gnomad4 AFR exome

AF:

0.556

Gnomad4 AMR exome

AF:

0.394

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.481

Gnomad4 SAS exome

AF:

0.305

Gnomad4 FIN exome

AF:

0.312

Gnomad4 NFE exome

AF:

0.303

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.409

AC:

62082

AN:

151874

Hom.:

13517

Cov.:

AF XY:

0.406

AC XY:

30146

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.575

Gnomad4 AMR

AF:

0.410

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.517

Gnomad4 SAS

AF:

0.288

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.410

Alfa

AF:

0.275

Hom.:

1400

Bravo

AF:

0.428

Asia WGS

AF:

0.354

AC:

1230

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.1

DANN

Benign

0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over