rs9387478

chr6-117465017-C-Achr6-117465017-C-T

Variant summary

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

The ENST00000525483.5(DCBLD1):n.81+11120C>A variant causes a intron, non coding transcript 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: DCBLD1 ENST00000525483.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

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=-0.96).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD1	ENST00000525483.5	n.81+11120C>A		intron_variant, non_coding_transcript_variant		4
DCBLD1	ENST00000528138.5	n.191+852C>A		intron_variant, non_coding_transcript_variant		4
DCBLD1	ENST00000533950.1	n.64+11120C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.553

Alfa AF: 0.494 Hom.: 10011

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

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: rs9387478; hg19: chr6-117786180;