rs1371687

chr3-98886146-A-Gchr3-98886146-A-T

Variant summary

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

The NM_080927.4(DCBLD2):c.206-4379T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,704 control chromosomes in the GnomAD database, including 8,765 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 0.32 (8765 hom., cov: 30)
• Consequence: DCBLD2 NM_080927.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.206-4379T>C		intron_variant		ENST00000326840.11
DCBLD2	XM_011512419.3	c.205+14976T>C		intron_variant
DCBLD2	XM_024453348.2	c.-114+4246T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.206-4379T>C		intron_variant		1	NM_080927.4	P1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47973 AN: 151586 Hom.: 8765 Cov.: 30

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.346

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.316 AC: 47982 AN: 151704 Hom.: 8765 Cov.: 30 AF XY: 0.321 AC XY: 23812 AN XY: 74114

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.347

Alfa AF: 0.317 Hom.: 1029

Bravo AF: 0.318

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.2
Dann	Benign	0.81

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: rs1371687; hg19: chr3-98604990;