6-117522909-A-G

Position:

• chr6-117522909-A-G

Variant summary

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

The NM_001366458.2(DCBLD1):​c.512+1333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,124 control chromosomes in the GnomAD database, including 39,970 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 0.71 (39970 hom., cov: 32)
• Consequence: DCBLD1 NM_001366458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD1	NM_001366458.2	c.512+1333A>G		intron_variant		ENST00000338728.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD1	ENST00000338728.10	c.512+1333A>G		intron_variant		5	NM_001366458.2	A2
DCBLD1	ENST00000296955.12	c.512+1333A>G		intron_variant		1		P2
DCBLD1	ENST00000533453.5	n.608+1333A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108653 AN: 152006 Hom.: 39930 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.715 AC: 108751 AN: 152124 Hom.: 39970 Cov.: 32 AF XY: 0.714 AC XY: 53112 AN XY: 74356

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.677

Alfa AF: 0.671 Hom.: 52198

Bravo AF: 0.706

Asia WGS AF: 0.578 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.54

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: rs210648; hg19: chr6-117844072; COSMIC: COSV51645547;