rs828616

Variant names:

• chr3-98822272-G-A
• rs828616
• NM_080927.4:c.786C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-98822272-G-A
• chr3-98822272-G-C
• chr3-98822272-G-T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_080927.4(DCBLD2):​c.786C>T​(p.Ile262Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,612,904 control chromosomes in the GnomAD database, including 106,864 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 0.31 (8642 hom., cov: 33)
  • Exomes 𝑓: 0.36 (98222 hom.)
• Consequence: DCBLD2 NM_080927.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• Publications: 21 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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BP7: Synonymous conserved (PhyloP=2.07 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCBLD2	NM_080927.4	c.786C>T	p.Ile262Ile	synonymous_variant	Exon 6 of 16	ENST00000326840.11	NP_563615.3
DCBLD2	XM_011512419.3	c.558C>T	p.Ile186Ile	synonymous_variant	Exon 5 of 15		XP_011510721.1
DCBLD2	XM_024453348.2	c.468C>T	p.Ile156Ile	synonymous_variant	Exon 6 of 16		XP_024309116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCBLD2	ENST00000326840.11	c.786C>T	p.Ile262Ile	synonymous_variant	Exon 6 of 16	1	NM_080927.4	ENSP00000321573.6
DCBLD2	ENST00000326857.9	c.786C>T	p.Ile262Ile	synonymous_variant	Exon 6 of 16	1		ENSP00000321646.9
DCBLD2	ENST00000469648.5	n.*37C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46911 AN: 151960 Hom.: 8642 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.340

GnomAD2 exomes AF: 0.393 AC: 97567 AN: 248176 AF XY: 0.392

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.532

Gnomad ASJ exome AF: 0.353

Gnomad EAS exome AF: 0.689

Gnomad FIN exome AF: 0.369

Gnomad NFE exome AF: 0.346

Gnomad OTH exome AF: 0.396

GnomAD4 exome AF: 0.357 AC: 521596 AN: 1460826 Hom.: 98222 Cov.: 39 AF XY: 0.359 AC XY: 260793 AN XY: 726716

African (AFR) AF: 0.110 AC: 3681 AN: 33472

American (AMR) AF: 0.520 AC: 23198 AN: 44646

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 9167 AN: 26122

East Asian (EAS) AF: 0.694 AC: 27541 AN: 39684

South Asian (SAS) AF: 0.404 AC: 34785 AN: 86198

European-Finnish (FIN) AF: 0.367 AC: 19597 AN: 53364

Middle Eastern (MID) AF: 0.343 AC: 1978 AN: 5764

European-Non Finnish (NFE) AF: 0.342 AC: 379983 AN: 1111226

Other (OTH) AF: 0.359 AC: 21666 AN: 60350

GnomAD4 genome AF: 0.309 AC: 46919 AN: 152078 Hom.: 8642 Cov.: 33 AF XY: 0.314 AC XY: 23354 AN XY: 74328

African (AFR) AF: 0.121 AC: 5042 AN: 41500

American (AMR) AF: 0.439 AC: 6719 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3544 AN: 5168

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4818

European-Finnish (FIN) AF: 0.373 AC: 3929 AN: 10542

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23412 AN: 67966

Other (OTH) AF: 0.341 AC: 721 AN: 2112

Alfa AF: 0.340 Hom.: 14940

Bravo AF: 0.309

Asia WGS AF: 0.523 AC: 1816 AN: 3478

EpiCase AF: 0.353

EpiControl AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	8.7
DANN	Benign	0.81
PhyloP100		2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs828616; hg19: chr3-98541116; COSMIC: COSV58789838; COSMIC: COSV58789838;