Variant 3-98799533-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000326840.11(DCBLD2):c.2167G>A(p.Asp723Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00663 in 1,613,970 control chromosomes in the GnomAD database, including 345 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.013 ( 59 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 286 hom. )

Consequence

DCBLD2
ENST00000326840.11 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.28

Variant links:

Genes affected

DCBLD2 (HGNC:24627): (discoidin, CUB and LCCL domain containing 2) Involved in negative regulation of cell growth and wound healing. Located in cell surface. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

DCBLD2 links:

ST3GAL6 (HGNC:):

ST3GAL6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017092526).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCBLD2	NM_080927.4 linkuse as main transcript	c.2167G>A	p.Asp723Asn	missense_variant	16/16	ENST00000326840.11	NP_563615.3	Q96PD2-1
DCBLD2	XM_011512419.3 linkuse as main transcript	c.1939G>A	p.Asp647Asn	missense_variant	15/15		XP_011510721.1
DCBLD2	XM_024453348.2 linkuse as main transcript	c.1849G>A	p.Asp617Asn	missense_variant	16/16		XP_024309116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DCBLD2	ENST00000326840.11 linkuse as main transcript	c.2167G>A	p.Asp723Asn	missense_variant	16/16	1	NM_080927.4	ENSP00000321573.6	Q96PD2-1
DCBLD2	ENST00000326857.9 linkuse as main transcript	c.2209G>A	p.Asp737Asn	missense_variant	16/16	1		ENSP00000321646.9	Q96PD2-2
ST3GAL6	ENST00000491912.1 linkuse as main transcript	n.254-1889C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0125

AC:

1897

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00357

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0635

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.0629

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.0291

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00112

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.0208

AC:

5184

AN:

249042

Hom.:

213

AF XY:

0.0167

AC XY:

2258

AN XY:

135096

show subpopulations

Gnomad AFR exome

AF:

0.00413

Gnomad AMR exome

AF:

0.0899

Gnomad ASJ exome

AF:

0.00169

Gnomad EAS exome

AF:

0.0613

Gnomad SAS exome

AF:

0.00173

Gnomad FIN exome

AF:

0.0289

Gnomad NFE exome

AF:

0.00127

Gnomad OTH exome

AF:

0.0129

GnomAD4 exome

AF:

0.00602

AC:

8793

AN:

1461694

Hom.:

286

Cov.:

AF XY:

0.00540

AC XY:

3930

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.00212

Gnomad4 AMR exome

AF:

0.0851

Gnomad4 ASJ exome

AF:

0.00145

Gnomad4 EAS exome

AF:

0.0537

Gnomad4 SAS exome

AF:

0.00209

Gnomad4 FIN exome

AF:

0.0271

Gnomad4 NFE exome

AF:

0.000468

Gnomad4 OTH exome

AF:

0.00990

GnomAD4 genome

AF:

0.0125

AC:

1907

AN:

152276

Hom.:

Cov.:

AF XY:

0.0149

AC XY:

1112

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00356

Gnomad4 AMR

AF:

0.0640

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.0631

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.0291

Gnomad4 NFE

AF:

0.00112

Gnomad4 OTH

AF:

0.0203

Alfa

AF:

0.00368

Hom.:

Bravo

AF:

0.0153

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.00354

AC:

ESP6500EA

AF:

0.000841

AC:

ExAC

AF:

0.0164

AC:

1982

Asia WGS

AF:

0.0440

AC:

153

AN:

3478

EpiCase

AF:

0.000600

EpiControl

AF:

0.000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.51

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.012

T;.

Eigen

Benign

0.14

Eigen_PC

Benign

0.21

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.81

T;T

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-0.84

MutationAssessor

Uncertain

2.7

M;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-2.0

N;N

REVEL

Benign

0.17

Sift

Uncertain

0.023

D;D

Sift4G

Benign

0.064

T;T

Polyphen

0.0030

B;D

Vest4

0.10

MPC

0.39

ClinPred

0.037

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.081

gMVP

0.48

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over