rs704586

chr3-98796317-G-A

Variant summary

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

The NM_080927.4(DCBLD2):c.*3055C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,224 control chromosomes in the GnomAD database, including 8,697 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 (8665 hom., cov: 32)
  • Exomes 𝑓: 0.37 (32 hom.)
• Consequence: DCBLD2 NM_080927.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

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

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 = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.*3055C>T		3_prime_UTR_variant	16/16	ENST00000326840.11
DCBLD2	XM_011512419.3	c.*3055C>T		3_prime_UTR_variant	15/15
DCBLD2	XM_024453348.2	c.*3055C>T		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.*3055C>T		3_prime_UTR_variant	16/16	1	NM_080927.4	P1
ST3GAL6	ENST00000491912.1	n.253+2525G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46942 AN: 151694 Hom.: 8664 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.368 AC: 154 AN: 418 Hom.: 32 Cov.: 0 AF XY: 0.366 AC XY: 93 AN XY: 254

Gnomad4 FIN exome AF: 0.373

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.309 AC: 46953 AN: 151806 Hom.: 8665 Cov.: 32 AF XY: 0.315 AC XY: 23372 AN XY: 74146

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.344

Alfa AF: 0.354 Hom.: 9798

Bravo AF: 0.310

Asia WGS AF: 0.537 AC: 1862 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.9
Dann	Benign	0.39

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: rs704586; hg19: chr3-98515161;