rs9285425

chr6-117550673-G-Achr6-117550673-G-T

Variant summary

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

The ENST00000296955.12(DCBLD1):c.1615+5076G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,990 control chromosomes in the GnomAD database, including 16,450 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 0.45 (16450 hom., cov: 32)
• Consequence: DCBLD1 ENST00000296955.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD1	NM_173674.3	c.1615+5076G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD1	ENST00000296955.12	c.1615+5076G>A		intron_variant		1		P2
DCBLD1	ENST00000533453.5	n.3345+5076G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68668 AN: 151872 Hom.: 16456 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.452 AC: 68693 AN: 151990 Hom.: 16450 Cov.: 32 AF XY: 0.459 AC XY: 34120 AN XY: 74300

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.454

Alfa AF: 0.489 Hom.: 3857

Bravo AF: 0.425

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.86

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: rs9285425; hg19: chr6-117871836; COSMIC: COSV51645677; COSMIC: COSV51645677;