6-117558532-C-T

Variant names:

• chr6-117558532-C-T
• rs916305
• ENST00000296955.12:c.1616-11088C>T

Variant summary

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

The NM_173674.3(DCBLD1):​c.1616-11088C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,176 control chromosomes in the GnomAD database, including 918 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 0.11 (918 hom., cov: 32)
• Consequence: DCBLD1 NM_173674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173674.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD1	NM_173674.3		c.1616-11088C>T		intron	N/A	NP_775945.1	Q8N8Z6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCBLD1	ENST00000296955.12	TSL:1	c.1616-11088C>T		intron	N/A	ENSP00000296955.8	Q8N8Z6-2
	ENSG00000282218	ENST00000467125.1	TSL:2	c.547+8322G>A		intron	N/A	ENSP00000487717.1	A0A0J9YVX5
	DCBLD1	ENST00000533453.5	TSL:1	n.3346-11088C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16039 AN: 152058 Hom.: 915 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.105 AC: 16046 AN: 152176 Hom.: 918 Cov.: 32 AF XY: 0.101 AC XY: 7546 AN XY: 74414

African (AFR) AF: 0.105 AC: 4372 AN: 41492

American (AMR) AF: 0.0871 AC: 1332 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3468

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5186

South Asian (SAS) AF: 0.0737 AC: 355 AN: 4820

European-Finnish (FIN) AF: 0.0793 AC: 839 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8165 AN: 68008

Other (OTH) AF: 0.101 AC: 213 AN: 2114

Alfa AF: 0.113 Hom.: 603

Bravo AF: 0.107

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.23
PhyloP100		0.25
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: rs916305; hg19: chr6-117879695;