rs793665

chr6-24363053-G-C

Variant summary

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

The NM_001195610.2(DCDC2):c.-97-5206C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0827 in 152,270 control chromosomes in the GnomAD database, including 650 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 0.083 (650 hom., cov: 32)
• Consequence: DCDC2 NM_001195610.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

DCDC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC2	NM_001195610.2	c.-97-5206C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12597 AN: 152152 Hom.: 650 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0827 AC: 12596 AN: 152270 Hom.: 650 Cov.: 32 AF XY: 0.0814 AC XY: 6060 AN XY: 74460

Gnomad4 AFR AF: 0.0266

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0886

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0972 Hom.: 110

Bravo AF: 0.0828

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs793665; hg19: chr6-24363281;