3-98869133-C-T

Position:

• chr3-98869133-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080927.4(DCBLD2):​c.433+12407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,930 control chromosomes in the GnomAD database, including 11,197 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 0.37 (11197 hom., cov: 32)
• Consequence: DCBLD2 NM_080927.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.433+12407G>A		intron_variant		ENST00000326840.11
DCBLD2	XM_011512419.3	c.206-19535G>A		intron_variant
DCBLD2	XM_024453348.2	c.115+12407G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.433+12407G>A		intron_variant		1	NM_080927.4	P1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55782 AN: 151808 Hom.: 11190 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.367 AC: 55803 AN: 151930 Hom.: 11197 Cov.: 32 AF XY: 0.372 AC XY: 27642 AN XY: 74238

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.394

Alfa AF: 0.399 Hom.: 25273

Bravo AF: 0.368

Asia WGS AF: 0.571 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs7615856; hg19: chr3-98587977;