rs916305

chr6-117558532-C-T

Variant summary

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

The ENST00000296955.12(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 ENST00000296955.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD1	NM_173674.3	c.1616-11088C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD1	ENST00000296955.12	c.1616-11088C>T		intron_variant		1		P2
DCBLD1	ENST00000533453.5	n.3346-11088C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.101

Alfa AF: 0.112 Hom.: 538

Bravo AF: 0.107

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.3
Dann	Benign	0.23

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: rs916305; hg19: chr6-117879695;