rs17574269

Positions:

• chr6-117494965-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001366458.2(DCBLD1):​c.113-8802A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 152,284 control chromosomes in the GnomAD database, including 83 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 0.031 (83 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: DCBLD1 NM_001366458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0306 (4652/152264) while in subpopulation NFE AF= 0.0375 (2552/68024). AF 95% confidence interval is 0.0363. There are 83 homozygotes in gnomad4. There are 2197 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 83 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD1	NM_001366458.2	c.113-8802A>G		intron_variant		ENST00000338728.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD1	ENST00000338728.10	c.113-8802A>G		intron_variant		5	NM_001366458.2	A2
DCBLD1	ENST00000296955.12	c.113-8802A>G		intron_variant		1		P2
DCBLD1	ENST00000525483.5	n.345-8802A>G		intron_variant, non_coding_transcript_variant		4
DCBLD1	ENST00000528162.1	n.346-8802A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4654 AN: 152146 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0330

GnomAD4 exome AF: 0.100 AC: 2 AN: 20 Hom.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.111

GnomAD4 genome AF: 0.0306 AC: 4652 AN: 152264 Hom.: 83 Cov.: 32 AF XY: 0.0295 AC XY: 2197 AN XY: 74456

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0255

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.0302

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0330 Hom.: 31

Bravo AF: 0.0301

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.66

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: rs17574269; hg19: chr6-117816128;