rs828618

Positions:

• chr3-98822789-G-A
• chr3-98822789-G-C

Variant summary

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

The NM_080927.4(DCBLD2):​c.624-48C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 1,493,708 control chromosomes in the GnomAD database, including 63,017 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 0.23 (5139 hom., cov: 33)
  • Exomes 𝑓: 0.29 (57878 hom.)
• Consequence: DCBLD2 NM_080927.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.624-48C>T		intron_variant		ENST00000326840.11
DCBLD2	XM_011512419.3	c.396-48C>T		intron_variant
DCBLD2	XM_024453348.2	c.306-48C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.624-48C>T		intron_variant		1	NM_080927.4	P1
DCBLD2	ENST00000326857.9	c.624-48C>T		intron_variant		1
DCBLD2	ENST00000469648.5	n.459-48C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35132 AN: 152008 Hom.: 5139 Cov.: 33

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.267

GnomAD3 exomes AF: 0.281 AC: 36276 AN: 128890 Hom.: 5550 AF XY: 0.285 AC XY: 19419 AN XY: 68034

Gnomad AFR exome AF: 0.0495

Gnomad AMR exome AF: 0.250

Gnomad ASJ exome AF: 0.285

Gnomad EAS exome AF: 0.423

Gnomad SAS exome AF: 0.276

Gnomad FIN exome AF: 0.314

Gnomad NFE exome AF: 0.290

Gnomad OTH exome AF: 0.306

GnomAD4 exome AF: 0.288 AC: 386397 AN: 1341580 Hom.: 57878 Cov.: 21 AF XY: 0.288 AC XY: 190687 AN XY: 661734

Gnomad4 AFR exome AF: 0.0453

Gnomad4 AMR exome AF: 0.243

Gnomad4 ASJ exome AF: 0.278

Gnomad4 EAS exome AF: 0.455

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.314

Gnomad4 NFE exome AF: 0.291

Gnomad4 OTH exome AF: 0.280

GnomAD4 genome AF: 0.231 AC: 35128 AN: 152128 Hom.: 5139 Cov.: 33 AF XY: 0.234 AC XY: 17371 AN XY: 74344

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.266

Alfa AF: 0.282 Hom.: 13340

Bravo AF: 0.221

Asia WGS AF: 0.352 AC: 1221 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	3.7
DANN	Benign	0.26

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: rs828618; hg19: chr3-98541633; COSMIC: COSV58794221; COSMIC: COSV58794221;