chr3-98822789-G-A

Variant names:

• chr3-98822789-G-A
• rs828618
• NM_080927.4:c.624-48C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080927.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD2	NM_080927.4	MANE Select	c.624-48C>T		intron	N/A	NP_563615.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD2	ENST00000326840.11	TSL:1 MANE Select	c.624-48C>T		intron	N/A	ENSP00000321573.6
	DCBLD2	ENST00000326857.9	TSL:1	c.624-48C>T		intron	N/A	ENSP00000321646.9
	DCBLD2	ENST00000469648.5	TSL:3	n.459-48C>T		intron	N/A

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

GnomAD2 exomes AF: 0.281 AC: 36276 AN: 128890 AF XY: 0.285

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 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

African (AFR) AF: 0.0453 AC: 1312 AN: 28970

American (AMR) AF: 0.243 AC: 6112 AN: 25122

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 6383 AN: 22938

East Asian (EAS) AF: 0.455 AC: 16152 AN: 35470

South Asian (SAS) AF: 0.272 AC: 19460 AN: 71492

European-Finnish (FIN) AF: 0.314 AC: 15329 AN: 48790

Middle Eastern (MID) AF: 0.277 AC: 1508 AN: 5440

European-Non Finnish (NFE) AF: 0.291 AC: 304617 AN: 1047826

Other (OTH) AF: 0.280 AC: 15524 AN: 55532

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

African (AFR) AF: 0.0551 AC: 2291 AN: 41546

American (AMR) AF: 0.274 AC: 4183 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2185 AN: 5162

South Asian (SAS) AF: 0.281 AC: 1357 AN: 4824

European-Finnish (FIN) AF: 0.327 AC: 3455 AN: 10576

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19737 AN: 67954

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.275 Hom.: 27011

Bravo AF: 0.221

Asia WGS AF: 0.352 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.26
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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