Genetic Variant DEPDC1:c.769+46_769+55delGTGTGTGTGT (chr1-68486881-AACACACACAC-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_001114120.3(DEPDC1):c.769+46_769+55delGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,177,044 control chromosomes in the GnomAD database, including 35 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.010 ( 28 hom., cov: 0)

Exomes 𝑓: 0.0014 ( 7 hom. )

Consequence

DEPDC1
NM_001114120.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.95

Publications

0 publications found

Variant links:

Genes affected

DEPDC1 (HGNC:22949): (DEP domain containing 1) Predicted to enable GTPase activator activity. Involved in negative regulation of transcription, DNA-templated. Located in nucleus. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

DEPDC1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0105 (1502/143728) while in subpopulation AFR AF = 0.0362 (1411/38942). AF 95% confidence interval is 0.0347. There are 28 homozygotes in GnomAd4. There are 706 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 28 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114120.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEPDC1	NM_001114120.3	MANE Select	c.769+46_769+55delGTGTGTGTGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+46_769+55delGTGTGTGTGT		intron	N/A	NP_060249.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DEPDC1	ENST00000456315.7	TSL:1 MANE Select	c.769+46_769+55delGTGTGTGTGT	intron	N/A	ENSP00000412292.2	Q5TB30-5
DEPDC1	ENST00000370966.9	TSL:1	c.769+46_769+55delGTGTGTGTGT	intron	N/A	ENSP00000360005.5	Q5TB30-2
DEPDC1	ENST00000489862.1	TSL:1	n.472+46_472+55delGTGTGTGTGT	intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes

AF:

0.0104

AC:

1490

AN:

143636

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0360

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00339

Gnomad ASJ

AF:

0.00567

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000684

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000764

Gnomad OTH

AF:

0.00865

GnomAD4 exome

AF:

0.00136

AC:

1405

AN:

1033316

Hom.:

AF XY:

0.00125

AC XY:

633

AN XY:

505320

show subpopulations

African (AFR)

AF:

0.0411

AC:

928

AN:

22590

American (AMR)

AF:

0.00184

AC:

AN:

17920

Ashkenazi Jewish (ASJ)

AF:

0.00486

AC:

AN:

15440

East Asian (EAS)

AF:

0.000165

AC:

AN:

30266

South Asian (SAS)

AF:

0.000298

AC:

AN:

30198

European-Finnish (FIN)

AF:

0.000121

AC:

AN:

41464

Middle Eastern (MID)

AF:

0.00422

AC:

AN:

3316

European-Non Finnish (NFE)

AF:

0.000253

AC:

210

AN:

829800

Other (OTH)

AF:

0.00298

AC:

126

AN:

42322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

133

178

222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.0105

AC:

1502

AN:

143728

Hom.:

Cov.:

AF XY:

0.0101

AC XY:

706

AN XY:

69602

show subpopulations

African (AFR)

AF:

0.0362

AC:

1411

AN:

38942

American (AMR)

AF:

0.00338

AC:

AN:

14190

Ashkenazi Jewish (ASJ)

AF:

0.00567

AC:

AN:

3350

East Asian (EAS)

AF:

0.00

AC:

AN:

4842

South Asian (SAS)

AF:

0.000457

AC:

AN:

4380

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9446

Middle Eastern (MID)

AF:

0.00

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.0000764

AC:

AN:

65420

Other (OTH)

AF:

0.00859

AC:

AN:

1980

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

135

203

270

338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00

Hom.:

278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.9

Mutation Taster

=100/0

polymorphism

(source)

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.

1-68486881-AACACACACACACACACACACACACACAC-AACACACACACACACACAC

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