chr3-98800637-G-A

Variant names:

• chr3-98800637-G-A
• rs1822017
• NM_080927.4:c.1800C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_080927.4(DCBLD2):​c.1800C>T​(p.Ser600Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,613,578 control chromosomes in the GnomAD database, including 20,568 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 0.17 (2463 hom., cov: 32)
  • Exomes 𝑓: 0.15 (18105 hom.)
• Consequence: DCBLD2 NM_080927.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 13 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]

ST3GAL6 (HGNC:18080): (ST3 beta-galactoside alpha-2,3-sialyltransferase 6) The protein encoded by this gene is a member of the sialyltransferase family. Members of this family are enzymes that transfer sialic acid from the activated cytidine 5'-monophospho-N-acetylneuraminic acid to terminal positions on sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins. This protein has high specificity for neolactotetraosylceramide and neolactohexaosylceramide as glycolipid substrates and may contribute to the formation of selectin ligands and sialyl Lewis X, a carbohydrate important for cell-to-cell recognition and a blood group antigen. [provided by RefSeq, Apr 2016]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP7: Synonymous conserved (PhyloP=0.024 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD2	NM_080927.4	MANE Select	c.1800C>T	p.Ser600Ser	synonymous	Exon 15 of 16	NP_563615.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD2	ENST00000326840.11	TSL:1 MANE Select	c.1800C>T	p.Ser600Ser	synonymous	Exon 15 of 16	ENSP00000321573.6	Q96PD2-1
	DCBLD2	ENST00000326857.9	TSL:1	c.1842C>T	p.Ser614Ser	synonymous	Exon 15 of 16	ENSP00000321646.9	Q96PD2-2
	DCBLD2	ENST00000946562.1		c.1662C>T	p.Ser554Ser	synonymous	Exon 14 of 15	ENSP00000616621.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26411 AN: 151888 Hom.: 2461 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.151

GnomAD2 exomes AF: 0.145 AC: 36048 AN: 249084 AF XY: 0.147

Gnomad AFR exome AF: 0.250

Gnomad AMR exome AF: 0.0776

Gnomad ASJ exome AF: 0.185

Gnomad EAS exome AF: 0.0431

Gnomad FIN exome AF: 0.122

Gnomad NFE exome AF: 0.158

Gnomad OTH exome AF: 0.149

GnomAD4 exome AF: 0.155 AC: 226143 AN: 1461574 Hom.: 18105 Cov.: 32 AF XY: 0.156 AC XY: 113267 AN XY: 727078

African (AFR) AF: 0.246 AC: 8221 AN: 33474

American (AMR) AF: 0.0839 AC: 3750 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 4963 AN: 26136

East Asian (EAS) AF: 0.0642 AC: 2548 AN: 39696

South Asian (SAS) AF: 0.180 AC: 15532 AN: 86246

European-Finnish (FIN) AF: 0.126 AC: 6747 AN: 53400

Middle Eastern (MID) AF: 0.195 AC: 1122 AN: 5768

European-Non Finnish (NFE) AF: 0.157 AC: 174233 AN: 1111770

Other (OTH) AF: 0.150 AC: 9027 AN: 60370

GnomAD4 genome AF: 0.174 AC: 26413 AN: 152004 Hom.: 2463 Cov.: 32 AF XY: 0.172 AC XY: 12766 AN XY: 74304

African (AFR) AF: 0.249 AC: 10319 AN: 41434

American (AMR) AF: 0.126 AC: 1919 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3468

East Asian (EAS) AF: 0.0467 AC: 241 AN: 5162

South Asian (SAS) AF: 0.178 AC: 858 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10574

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10433 AN: 67970

Other (OTH) AF: 0.151 AC: 318 AN: 2110

Alfa AF: 0.165 Hom.: 3398

Bravo AF: 0.176

Asia WGS AF: 0.130 AC: 454 AN: 3478

EpiCase AF: 0.161

EpiControl AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	3.3
DANN	Benign	0.82
PhyloP100		0.024
Mutation Taster		=97/3	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: rs1822017; hg19: chr3-98519481; COSMIC: COSV54578801; COSMIC: COSV54578801;