rs1062196

Positions:

• chr3-98798169-T-C
• chr3-98798169-T-G

Variant summary

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

The NM_080927.4(DCBLD2):​c.*1203A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,094 control chromosomes in the GnomAD database, including 14,581 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 0.44 (14581 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: DCBLD2 NM_080927.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCBLD2	NM_080927.4	c.*1203A>G		3_prime_UTR_variant	16/16	ENST00000326840.11	NP_563615.3
DCBLD2	XM_011512419.3	c.*1203A>G		3_prime_UTR_variant	15/15		XP_011510721.1
DCBLD2	XM_024453348.2	c.*1203A>G		3_prime_UTR_variant	16/16		XP_024309116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCBLD2	ENST00000326840.11	c.*1203A>G		3_prime_UTR_variant	16/16	1	NM_080927.4	ENSP00000321573	P1
DCBLD2	ENST00000326857.9	c.*1203A>G		3_prime_UTR_variant	16/16	1		ENSP00000321646
ST3GAL6	ENST00000491912.1	n.254-3253T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66106 AN: 151976 Hom.: 14558 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.439

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.435 AC: 66164 AN: 152094 Hom.: 14581 Cov.: 32 AF XY: 0.432 AC XY: 32082 AN XY: 74340

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.435

Alfa AF: 0.428 Hom.: 17370

Bravo AF: 0.430

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60

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: rs1062196; hg19: chr3-98517013;