Variant 11-47214743-A-G 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_001399874.1(DDB2):c.-67+69A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 321,550 control chromosomes in the GnomAD database, including 79,933 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.69 ( 36418 hom., cov: 26)

Exomes 𝑓: 0.70 ( 43515 hom. )

Consequence

DDB2
NM_001399874.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.78

Variant links:

Genes affected

DDB2 (HGNC:2718): (damage specific DNA binding protein 2) This gene encodes a protein that is necessary for the repair of ultraviolet light-damaged DNA. This protein is the smaller subunit of a heterodimeric protein complex that participates in nucleotide excision repair, and this complex mediates the ubiquitylation of histones H3 and H4, which facilitates the cellular response to DNA damage. This subunit appears to be required for DNA binding. Mutations in this gene cause xeroderma pigmentosum complementation group E, a recessive disease that is characterized by an increased sensitivity to UV light and a high predisposition for skin cancer development, in some cases accompanied by neurological abnormalities. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

DDB2 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=-0.99).

BP6

Variant 11-47214743-A-G is Benign according to our data. Variant chr11-47214743-A-G is described in ClinVar as [Benign]. Clinvar id is 1287348.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
DDB2	NM_001399874.1 linkuse as main transcript	c.-67+69A>G	intron_variant	NP_001386803.1
DDB2	NM_001399875.1 linkuse as main transcript	c.-65+69A>G	intron_variant	NP_001386804.1
DDB2	NM_001399876.1 linkuse as main transcript	c.-67+69A>G	intron_variant	NP_001386805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDB2	ENST00000614825.4 linkuse as main transcript	c.-65+69A>G		intron_variant		3		ENSP00000483718
DDB2	ENST00000622878.4 linkuse as main transcript	c.-67+69A>G		intron_variant		4		ENSP00000479196

Frequencies

GnomAD3 genomes

AF:

0.693

AC:

103658

AN:

149604

Hom.:

36411

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.719

Gnomad AMR

AF:

0.667

Gnomad ASJ

AF:

0.808

Gnomad EAS

AF:

0.355

Gnomad SAS

AF:

0.714

Gnomad FIN

AF:

0.637

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.724

GnomAD4 exome

AF:

0.697

AC:

119791

AN:

171846

Hom.:

43515

Cov.:

AF XY:

0.695

AC XY:

63363

AN XY:

91220

show subpopulations

Gnomad4 AFR exome

AF:

0.623

Gnomad4 AMR exome

AF:

0.577

Gnomad4 ASJ exome

AF:

0.794

Gnomad4 EAS exome

AF:

0.324

Gnomad4 SAS exome

AF:

0.685

Gnomad4 FIN exome

AF:

0.653

Gnomad4 NFE exome

AF:

0.753

Gnomad4 OTH exome

AF:

0.718

GnomAD4 genome

AF:

0.693

AC:

103701

AN:

149704

Hom.:

36418

Cov.:

AF XY:

0.686

AC XY:

50021

AN XY:

72952

show subpopulations

Gnomad4 AFR

AF:

0.643

Gnomad4 AMR

AF:

0.667

Gnomad4 ASJ

AF:

0.808

Gnomad4 EAS

AF:

0.354

Gnomad4 SAS

AF:

0.713

Gnomad4 FIN

AF:

0.637

Gnomad4 NFE

AF:

0.753

Gnomad4 OTH

AF:

0.729

Alfa

AF:

0.708

Hom.:

4554

Bravo

AF:

0.688

Asia WGS

AF:

0.614

AC:

2137

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

Jan 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.1

DANN

Benign

0.15

Splicing

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