chr6-117498194-A-G

Position:

• chr6-117498194-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.113-5573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,026 control chromosomes in the GnomAD database, including 29,241 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 0.60 (29241 hom., cov: 32)
• Consequence: DCBLD1 NM_001366458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

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 = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCBLD1	NM_001366458.2	c.113-5573A>G		intron_variant		ENST00000338728.10	NP_001353387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCBLD1	ENST00000338728.10	c.113-5573A>G		intron_variant		5	NM_001366458.2	ENSP00000342422	A2
DCBLD1	ENST00000296955.12	c.113-5573A>G		intron_variant		1		ENSP00000296955	P2
DCBLD1	ENST00000525483.5	n.345-5573A>G		intron_variant, non_coding_transcript_variant		4
DCBLD1	ENST00000528162.1	n.346-5573A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91103 AN: 151910 Hom.: 29195 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.600 AC: 91204 AN: 152026 Hom.: 29241 Cov.: 32 AF XY: 0.601 AC XY: 44624 AN XY: 74280

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.561

Alfa AF: 0.543 Hom.: 5504

Bravo AF: 0.598

Asia WGS AF: 0.557 AC: 1936 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	0.30
DANN	Benign	0.61

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: rs2057314; hg19: chr6-117819357; COSMIC: COSV51645439; COSMIC: COSV51645439;