rs3796133

chr3-98798999-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.*373C>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 0.0501 in 179,372 control chromosomes in the GnomAD database, including 238 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 0.052 (210 hom., cov: 32)
  • Exomes 𝑓: 0.042 (28 hom.)
• Consequence: DCBLD2 NM_080927.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.*373C>T		3_prime_UTR_variant	16/16	ENST00000326840.11
DCBLD2	XM_011512419.3	c.*373C>T		3_prime_UTR_variant	15/15
DCBLD2	XM_024453348.2	c.*373C>T		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.*373C>T		3_prime_UTR_variant	16/16	1	NM_080927.4	P1
DCBLD2	ENST00000326857.9	c.*373C>T		3_prime_UTR_variant	16/16	1
ST3GAL6	ENST00000491912.1	n.254-2423G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0516 AC: 7841 AN: 152096 Hom.: 209 Cov.: 32

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0468

GnomAD4 exome AF: 0.0421 AC: 1142 AN: 27158 Hom.: 28 Cov.: 0 AF XY: 0.0431 AC XY: 597 AN XY: 13842

Gnomad4 AFR exome AF: 0.0617

Gnomad4 AMR exome AF: 0.0306

Gnomad4 ASJ exome AF: 0.0427

Gnomad4 EAS exome AF: 0.0265

Gnomad4 SAS exome AF: 0.0288

Gnomad4 FIN exome AF: 0.0563

Gnomad4 NFE exome AF: 0.0446

Gnomad4 OTH exome AF: 0.0481

GnomAD4 genome AF: 0.0516 AC: 7850 AN: 152214 Hom.: 210 Cov.: 32 AF XY: 0.0512 AC XY: 3811 AN XY: 74434

Gnomad4 AFR AF: 0.0675

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.0639

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0467 Hom.: 280

Bravo AF: 0.0508

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.6
Dann	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3796133; hg19: chr3-98517843;