chr6-117465017-C-A

Variant names:

• chr6-117465017-C-A
• rs9387478
• ENST00000467125.1:c.547+101837G>T

Variant summary

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

The ENST00000467125.1(ENSG00000282218):​c.547+101837G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,044 control chromosomes in the GnomAD database, including 29,122 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 (29122 hom., cov: 32)
• Consequence: ENSG00000282218 ENST00000467125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 48 publications found

Genes affected

ENSG00000282218 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282218	ENST00000467125.1	c.547+101837G>T		intron_variant	Intron 4 of 6	2		ENSP00000487717.1
DCBLD1	ENST00000525483.5	n.81+11120C>A		intron_variant	Intron 1 of 3	4
DCBLD1	ENST00000528138.5	n.191+852C>A		intron_variant	Intron 2 of 4	4
DCBLD1	ENST00000533950.1	n.64+11120C>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90595 AN: 151926 Hom.: 29075 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.597 AC: 90707 AN: 152044 Hom.: 29122 Cov.: 32 AF XY: 0.599 AC XY: 44513 AN XY: 74294

African (AFR) AF: 0.853 AC: 35398 AN: 41512

American (AMR) AF: 0.452 AC: 6892 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1510 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2559 AN: 5166

South Asian (SAS) AF: 0.685 AC: 3301 AN: 4816

European-Finnish (FIN) AF: 0.586 AC: 6179 AN: 10546

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33016 AN: 67958

Other (OTH) AF: 0.553 AC: 1166 AN: 2108

Alfa AF: 0.517 Hom.: 48031

Bravo AF: 0.592

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.55
PhyloP100		-0.41

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: rs9387478; hg19: chr6-117786180;