6-24174451-T-TTACAAA

Position:

• chr6-24174451-T-TTACAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_016356.5(DCDC2):​c.*278_*279insTTTGTA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (10995 hom., cov: 0)
  • Exomes 𝑓: 0.24 (2853 hom.)
• Consequence: DCDC2 NM_016356.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.188

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 -10 ACMG points.

• BP6: Variant 6-24174451-T-TTACAAA is Benign according to our data. Variant chr6-24174451-T-TTACAAA is described in ClinVar as [Benign]. Clinvar id is 1224735.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC2	NM_016356.5	c.*278_*279insTTTGTA		3_prime_UTR_variant	10/10	ENST00000378454.8	NP_057440.2
DCDC2	NM_001195610.2	c.*278_*279insTTTGTA		3_prime_UTR_variant	11/11		NP_001182539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC2	ENST00000378454	c.*278_*279insTTTGTA		3_prime_UTR_variant	10/10	1	NM_016356.5	ENSP00000367715.3
DCDC2	ENST00000378450	c.*278_*279insTTTGTA		3_prime_UTR_variant	3/3	1		ENSP00000367711.3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51151 AN: 151526 Hom.: 10983 Cov.: 0

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.235 AC: 18039 AN: 76622 Hom.: 2853 Cov.: 0 AF XY: 0.232 AC XY: 9294 AN XY: 39998

Gnomad4 AFR exome AF: 0.595

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.237

Gnomad4 EAS exome AF: 0.537

Gnomad4 SAS exome AF: 0.241

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.181

Gnomad4 OTH exome AF: 0.245

GnomAD4 genome AF: 0.338 AC: 51215 AN: 151648 Hom.: 10995 Cov.: 0 AF XY: 0.337 AC XY: 24976 AN XY: 74140

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.298

Alfa AF: 0.288 Hom.: 857

Bravo AF: 0.364

Asia WGS AF: 0.425 AC: 1476 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

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3833459; hg19: chr6-24174679;