rs1091047

chr6-24295028-C-Gchr6-24295028-C-T

Variant summary

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

The NM_016356.5(DCDC2):c.558-3950G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,766 control chromosomes in the GnomAD database, including 4,054 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 0.21 (4054 hom., cov: 31)
• Consequence: DCDC2 NM_016356.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC2	NM_016356.5	c.558-3950G>C		intron_variant		ENST00000378454.8
DCDC2	NM_001195610.2	c.558-3950G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC2	ENST00000378454.8	c.558-3950G>C		intron_variant		1	NM_016356.5	P1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32119 AN: 151648 Hom.: 4046 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0840

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.212 AC: 32167 AN: 151766 Hom.: 4054 Cov.: 31 AF XY: 0.210 AC XY: 15605 AN XY: 74196

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0840

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.179

Alfa AF: 0.0696 Hom.: 68

Bravo AF: 0.220

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	9.8
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs1091047; hg19: chr6-24295256;