6-24360961-C-G

Position:

• chr6-24360961-C-G

Variant summary

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

The NM_001195610.2(DCDC2):​c.-97-3114G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,862 control chromosomes in the GnomAD database, including 15,535 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 0.43 (15535 hom., cov: 32)
• Consequence: DCDC2 NM_001195610.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

Genes affected

DCDC2 (HGNC:18141): (doublecortin domain containing 2) This gene encodes a doublecortin domain-containing family member. The doublecortin domain has been demonstrated to bind tubulin and enhance microtubule polymerization. This family member is thought to function in neuronal migration where it may affect the signaling of primary cilia. Mutations in this gene have been associated with reading disability (RD) type 2, also referred to as developmental dyslexia. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jan 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC2	NM_001195610.2	c.-97-3114G>C		intron_variant			NP_001182539.1
		n.24360961C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65474 AN: 151744 Hom.: 15543 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.431 AC: 65464 AN: 151862 Hom.: 15535 Cov.: 32 AF XY: 0.433 AC XY: 32111 AN XY: 74210

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.450

Alfa AF: 0.340 Hom.: 989

Bravo AF: 0.418

Asia WGS AF: 0.415 AC: 1446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2792666; hg19: chr6-24361189;