Genetic Variant DCDC1:c.5234-9_5234-6delTTTT (chr11-30878716-TAAAA-T) – 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.5234-9_5234-6delTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000342 in 1,248,748 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00034 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DCDC1
NM_001387274.1 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

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:

Genome browser will be placed here

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.5234-9_5234-6delTTTT	splice_region intron	N/A	NP_001374203.1	A0A804HJA9
DCDC1	NM_001367979.1		c.5225-9_5225-6delTTTT	splice_region intron	N/A	NP_001354908.1	M0R2J8-1
DCDC1	NM_020869.4		c.2546-9_2546-6delTTTT	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.5234-9_5234-6delTTTT	splice_region intron	N/A	ENSP00000507427.1	A0A804HJA9
DCDC1	ENST00000597505.5	TSL:5	c.5225-9_5225-6delTTTT	splice_region intron	N/A	ENSP00000472625.1	M0R2J8-1
DCDC1	ENST00000406071.6	TSL:5	c.2546-9_2546-6delTTTT	splice_region intron	N/A	ENSP00000385936.3	B6ZDN3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

140188

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00112

AC:

128

AN:

114698

AF XY:

0.00123

show subpopulations

Gnomad AFR exome

AF:

0.000733

Gnomad AMR exome

AF:

0.00102

Gnomad ASJ exome

AF:

0.00302

Gnomad EAS exome

AF:

0.000377

Gnomad FIN exome

AF:

0.000444

Gnomad NFE exome

AF:

0.00112

Gnomad OTH exome

AF:

0.000829

GnomAD4 exome

AF:

0.000342

AC:

427

AN:

1248748

Hom.:

AF XY:

0.000407

AC XY:

252

AN XY:

618988

show subpopulations

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

African (AFR)

AF:

0.000266

AC:

AN:

26332

American (AMR)

AF:

0.00105

AC:

AN:

23876

Ashkenazi Jewish (ASJ)

AF:

0.000720

AC:

AN:

19440

East Asian (EAS)

AF:

0.000118

AC:

AN:

33786

South Asian (SAS)

AF:

0.000870

AC:

AN:

65502

European-Finnish (FIN)

AF:

0.000316

AC:

AN:

41114

Middle Eastern (MID)

AF:

0.000228

AC:

AN:

4388

European-Non Finnish (NFE)

AF:

0.000298

AC:

293

AN:

983030

Other (OTH)

AF:

0.000254

AC:

AN:

51280

⚠️ 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: 0.254

Heterozygous variant carriers

107

160

214

267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

140188

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

67790

African (AFR)

AF:

0.00

AC:

AN:

37312

American (AMR)

AF:

0.00

AC:

AN:

13966

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3380

East Asian (EAS)

AF:

0.00

AC:

AN:

4768

South Asian (SAS)

AF:

0.00

AC:

AN:

4378

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8244

Middle Eastern (MID)

AF:

0.00

AC:

AN:

296

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

65070

Other (OTH)

AF:

0.00

AC:

AN:

1898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

11-30878716-TAAAAAA-TAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over