rs9320607

Variant names:

• chr6-117535708-C-T
• rs9320607
• NM_001366458.2:c.720-1477C>T

Variant summary

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

The NM_001366458.2(DCBLD1):​c.720-1477C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0416 in 152,010 control chromosomes in the GnomAD database, including 275 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 0.042 (275 hom., cov: 32)
• Consequence: DCBLD1 NM_001366458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

DCBLD1 (HGNC:21479): (discoidin, CUB and LCCL domain containing 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000282218 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCBLD1	NM_001366458.2	c.720-1477C>T		intron_variant	Intron 6 of 14	ENST00000338728.10	NP_001353387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCBLD1	ENST00000338728.10	c.720-1477C>T		intron_variant	Intron 6 of 14	5	NM_001366458.2	ENSP00000342422.6
DCBLD1	ENST00000296955.12	c.720-1477C>T		intron_variant	Intron 6 of 14	1		ENSP00000296955.8
ENSG00000282218	ENST00000467125.1	c.547+31146G>A		intron_variant	Intron 4 of 6	2		ENSP00000487717.1
DCBLD1	ENST00000533453.5	n.743-1477C>T		intron_variant	Intron 4 of 10	1

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6298 AN: 151892 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0235

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00653

Gnomad OTH AF: 0.0412

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

GnomAD4 genome AF: 0.0416 AC: 6327 AN: 152010 Hom.: 275 Cov.: 32 AF XY: 0.0424 AC XY: 3150 AN XY: 74266

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0936

Gnomad4 SAS AF: 0.0182

Gnomad4 FIN AF: 0.0235

Gnomad4 NFE AF: 0.00653

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0366 Hom.: 28

Bravo AF: 0.0448

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.87

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: rs9320607; hg19: chr6-117856871;