6-24277772-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_016356.5(DCDC2):c.922+277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 151,780 control chromosomes in the GnomAD database, including 40,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.71 (40352 hom., cov: 31)
• Consequence: DCDC2 NM_016356.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.662

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 6-24277772-A-G is Benign according to our data. Variant chr6-24277772-A-G is described in ClinVar as [Benign]. Clinvar id is 1228842.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC2	NM_016356.5	c.922+277T>C		intron_variant		ENST00000378454.8
DCDC2	NM_001195610.2	c.922+277T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC2	ENST00000378454.8	c.922+277T>C		intron_variant		1	NM_016356.5	P1

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108409 AN: 151662 Hom.: 40337 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.715 AC: 108467 AN: 151780 Hom.: 40352 Cov.: 31 AF XY: 0.723 AC XY: 53633 AN XY: 74178

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.699

Alfa AF: 0.733 Hom.: 5227

Bravo AF: 0.693

Asia WGS AF: 0.846 AC: 2940 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.6
Dann	Benign	0.62

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: rs807726; hg19: chr6-24278000;