Genetic Variant DCDC1:c.5234-6dupT (chr11-30878716-T-TA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001387274.1(DCDC1):c.5234-6dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0035 ( 1 hom., cov: 0)

Exomes 𝑓: 0.010 ( 0 hom. )

Consequence

DCDC1
NM_001387274.1 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.697

Publications

1 publications found

Variant links:

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 links:

ENSG00000287373 (HGNC:):

ENSG00000287373 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387274.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DCDC1	NM_001387274.1	MANE Select	c.5234-6dupT	splice_region intron	N/A	NP_001374203.1	A0A804HJA9
DCDC1	NM_001367979.1		c.5225-6dupT	splice_region intron	N/A	NP_001354908.1	M0R2J8-1
DCDC1	NM_020869.4		c.2546-6dupT	splice_region intron	N/A	NP_065920.2	B6ZDN3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DCDC1	ENST00000684477.1	MANE Select	c.5234-6_5234-5insT	splice_region intron	N/A	ENSP00000507427.1	A0A804HJA9
DCDC1	ENST00000597505.5	TSL:5	c.5225-6_5225-5insT	splice_region intron	N/A	ENSP00000472625.1	M0R2J8-1
DCDC1	ENST00000406071.6	TSL:5	c.2546-6_2546-5insT	splice_region intron	N/A	ENSP00000385936.3	B6ZDN3

Frequencies

GnomAD3 genomes

AF:

0.00350

AC:

490

AN:

140176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00824

Gnomad ASJ

AF:

0.00207

Gnomad EAS

AF:

0.00252

Gnomad SAS

AF:

0.00594

Gnomad FIN

AF:

0.000728

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00121

Gnomad OTH

AF:

0.00580

GnomAD2 exomes

AF:

0.00922

AC:

1058

AN:

114698

AF XY:

0.00894

show subpopulations

Gnomad AFR exome

AF:

0.0163

Gnomad AMR exome

AF:

0.0183

Gnomad ASJ exome

AF:

0.00740

Gnomad EAS exome

AF:

0.0157

Gnomad FIN exome

AF:

0.00800

Gnomad NFE exome

AF:

0.00567

Gnomad OTH exome

AF:

0.00829

GnomAD4 exome

AF:

0.0104

AC:

12969

AN:

1243136

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

6382

AN XY:

616370

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0230

AC:

600

AN:

26084

American (AMR)

AF:

0.0187

AC:

444

AN:

23780

Ashkenazi Jewish (ASJ)

AF:

0.00814

AC:

158

AN:

19412

East Asian (EAS)

AF:

0.0160

AC:

537

AN:

33588

South Asian (SAS)

AF:

0.0156

AC:

1019

AN:

65280

European-Finnish (FIN)

AF:

0.0107

AC:

438

AN:

40962

Middle Eastern (MID)

AF:

0.00801

AC:

AN:

4372

European-Non Finnish (NFE)

AF:

0.00935

AC:

9148

AN:

978570

Other (OTH)

AF:

0.0115

AC:

590

AN:

51088

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.284

Heterozygous variant carriers

1047

2094

3142

4189

5236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

380

760

1140

1520

1900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00350

AC:

491

AN:

140222

Hom.:

Cov.:

AF XY:

0.00371

AC XY:

252

AN XY:

67844

show subpopulations

African (AFR)

AF:

0.00629

AC:

235

AN:

37388

American (AMR)

AF:

0.00822

AC:

115

AN:

13984

Ashkenazi Jewish (ASJ)

AF:

0.00207

AC:

AN:

3380

East Asian (EAS)

AF:

0.00253

AC:

AN:

4752

South Asian (SAS)

AF:

0.00597

AC:

AN:

4358

European-Finnish (FIN)

AF:

0.000728

AC:

AN:

8244

Middle Eastern (MID)

AF:

0.00

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.00121

AC:

AN:

65054

Other (OTH)

AF:

0.00575

AC:

AN:

1914

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00118

Hom.:

578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.70

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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11-30878716-TAAAAAA-TAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over