11-30878716-TAA-T

Position:

• chr11-30878716-TAA-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_001387274.1(DCDC1):​c.5234-7_5234-6delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,325,020 control chromosomes in the GnomAD database, including 74 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.019 (66 hom., cov: 0)
  • Exomes 𝑓: 0.13 (8 hom.)
• Consequence: DCDC1 NM_001387274.1 splice_region, intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.838

Genes affected

DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]

DCDC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 11-30878716-TAA-T is Benign according to our data. Variant chr11-30878716-TAA-T is described in ClinVar as [Benign]. Clinvar id is 3347052.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.5234-7_5234-6delTT		splice_region_variant, intron_variant		ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.5234-7_5234-6delTT		splice_region_variant, intron_variant			NM_001387274.1	ENSP00000507427.1

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2642 AN: 140068 Hom.: 65 Cov.: 0

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00781

Gnomad ASJ AF: 0.00207

Gnomad EAS AF: 0.000419

Gnomad SAS AF: 0.00183

Gnomad FIN AF: 0.00999

Gnomad MID AF: 0.0136

Gnomad NFE AF: 0.00323

Gnomad OTH AF: 0.0200

GnomAD3 exomes AF: 0.146 AC: 16711 AN: 114698 Hom.: 10 AF XY: 0.153 AC XY: 9727 AN XY: 63428

Gnomad AFR exome AF: 0.106

Gnomad AMR exome AF: 0.111

Gnomad ASJ exome AF: 0.212

Gnomad EAS exome AF: 0.0781

Gnomad SAS exome AF: 0.179

Gnomad FIN exome AF: 0.105

Gnomad NFE exome AF: 0.164

Gnomad OTH exome AF: 0.149

GnomAD4 exome AF: 0.125 AC: 148584 AN: 1184910 Hom.: 8 AF XY: 0.129 AC XY: 75617 AN XY: 587788

Gnomad4 AFR exome AF: 0.0989

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.178

Gnomad4 EAS exome AF: 0.0832

Gnomad4 SAS exome AF: 0.149

Gnomad4 FIN exome AF: 0.121

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.126

GnomAD4 genome AF: 0.0189 AC: 2647 AN: 140110 Hom.: 66 Cov.: 0 AF XY: 0.0183 AC XY: 1240 AN XY: 67780

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.00780

Gnomad4 ASJ AF: 0.00207

Gnomad4 EAS AF: 0.000421

Gnomad4 SAS AF: 0.00161

Gnomad4 FIN AF: 0.00999

Gnomad4 NFE AF: 0.00323

Gnomad4 OTH AF: 0.0199

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

DCDC5-related condition Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 15, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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: rs5790842; hg19: chr11-30900263;