6-117498194-A-G

Variant names:

• chr6-117498194-A-G
• rs2057314
• NM_001366458.2:c.113-5573A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366458.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD1	NM_001366458.2	MANE Select	c.113-5573A>G		intron	N/A	NP_001353387.1
	DCBLD1	NM_173674.3		c.113-5573A>G		intron	N/A	NP_775945.1
	DCBLD1	NM_001366459.2		c.113-5573A>G		intron	N/A	NP_001353388.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD1	ENST00000338728.10	TSL:5 MANE Select	c.113-5573A>G		intron	N/A	ENSP00000342422.6
	DCBLD1	ENST00000296955.12	TSL:1	c.113-5573A>G		intron	N/A	ENSP00000296955.8
	ENSG00000282218	ENST00000467125.1	TSL:2	c.547+68660T>C		intron	N/A	ENSP00000487717.1

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

African (AFR) AF: 0.849 AC: 35224 AN: 41488

American (AMR) AF: 0.460 AC: 7029 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2445 AN: 5168

South Asian (SAS) AF: 0.614 AC: 2959 AN: 4818

European-Finnish (FIN) AF: 0.602 AC: 6329 AN: 10514

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33805 AN: 67958

Other (OTH) AF: 0.561 AC: 1187 AN: 2116

Alfa AF: 0.538 Hom.: 40180

Bravo AF: 0.598

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.61
PhyloP100		-0.69
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: rs2057314; hg19: chr6-117819357; COSMIC: COSV51645439; COSMIC: COSV51645439;