rs828621

Variant names:

• chr3-98824818-T-A
• rs828621
• NM_080927.4:c.623+497A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-98824818-T-A
• chr3-98824818-T-C
• chr3-98824818-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080927.4(DCBLD2):​c.623+497A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,810 control chromosomes in the GnomAD database, including 11,010 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 0.36 (11010 hom., cov: 31)
• Consequence: DCBLD2 NM_080927.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCBLD2	NM_080927.4	c.623+497A>T		intron_variant	Intron 4 of 15	ENST00000326840.11	NP_563615.3
DCBLD2	XM_011512419.3	c.395+497A>T		intron_variant	Intron 3 of 14		XP_011510721.1
DCBLD2	XM_024453348.2	c.305+497A>T		intron_variant	Intron 4 of 15		XP_024309116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCBLD2	ENST00000326840.11	c.623+497A>T		intron_variant	Intron 4 of 15	1	NM_080927.4	ENSP00000321573.6
DCBLD2	ENST00000326857.9	c.623+497A>T		intron_variant	Intron 4 of 15	1		ENSP00000321646.9
DCBLD2	ENST00000469648.5	n.458+497A>T		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54754 AN: 151692 Hom.: 11004 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.361 AC: 54772 AN: 151810 Hom.: 11010 Cov.: 31 AF XY: 0.366 AC XY: 27161 AN XY: 74174

African (AFR) AF: 0.192 AC: 7936 AN: 41404

American (AMR) AF: 0.474 AC: 7222 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1355 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3669 AN: 5144

South Asian (SAS) AF: 0.458 AC: 2200 AN: 4808

European-Finnish (FIN) AF: 0.435 AC: 4565 AN: 10492

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26532 AN: 67938

Other (OTH) AF: 0.390 AC: 821 AN: 2106

Alfa AF: 0.235 Hom.: 573

Bravo AF: 0.361

Asia WGS AF: 0.574 AC: 1992 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	0.14
DANN	Benign	0.74
PhyloP100		-0.70
Mutation Taster		=100/0	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: rs828621; hg19: chr3-98543662;