Genetic Variant DEPP1:c.*795T>C (chr10-44976597-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007021.4(DEPP1):c.*795T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,644 control chromosomes in the GnomAD database, including 40,584 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.73 ( 40461 hom., cov: 33)

Exomes 𝑓: 0.72 ( 123 hom. )

Consequence

DEPP1
NM_007021.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

9 publications found

Variant links:

Genes affected

DEPP1 (HGNC:23355): (DEPP autophagy regulator 1) The expression of this gene is induced by fasting as well as by progesterone. The protein encoded by this gene contains a t-synaptosome-associated protein receptor (SNARE) coiled-coil homology domain and a peroxisomal targeting signal. Production of the encoded protein leads to phosphorylation and activation of the transcription factor ELK1. [provided by RefSeq, Jul 2008]

DEPP1 links:

RASSF4 (HGNC:20793): (Ras association domain family member 4) The function of this gene has not yet been determined but may involve a role in tumor suppression. Alternative splicing of this gene results in several transcript variants; however, most of the variants have not been fully described. [provided by RefSeq, Jul 2008]

RASSF4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEPP1	NM_007021.4 link	c.*795T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000298295.4	NP_008952.1	Q9NTK1
RASSF4	NM_032023.4 link	c.138+4749A>G		intron_variant	Intron 3 of 10	ENST00000340258.10	NP_114412.2	Q9H2L5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPP1	ENST00000298295.4 link	c.*795T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_007021.4	ENSP00000298295.3		Q9NTK1
RASSF4	ENST00000340258.10 link	c.138+4749A>G		intron_variant	Intron 3 of 10	1	NM_032023.4	ENSP00000339692.4		Q9H2L5-1

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110738

AN:

152072

Hom.:

40418

Cov.:

show subpopulations

Gnomad AFR

AF:

0.720

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.784

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.764

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.719

Gnomad OTH

AF:

0.725

GnomAD4 exome

AF:

0.722

AC:

328

AN:

454

Hom.:

123

Cov.:

AF XY:

0.738

AC XY:

242

AN XY:

328

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.667

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.800

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.625

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.729

AC:

258

AN:

354

Other (OTH)

AF:

0.700

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.728

AC:

110843

AN:

152190

Hom.:

40461

Cov.:

AF XY:

0.733

AC XY:

54514

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.720

AC:

29893

AN:

41530

American (AMR)

AF:

0.784

AC:

11993

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.634

AC:

2200

AN:

3470

East Asian (EAS)

AF:

0.776

AC:

4017

AN:

5176

South Asian (SAS)

AF:

0.762

AC:

3674

AN:

4822

European-Finnish (FIN)

AF:

0.749

AC:

7927

AN:

10584

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.719

AC:

48911

AN:

67998

Other (OTH)

AF:

0.728

AC:

1537

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1612

3224

4837

6449

8061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

846

1692

2538

3384

4230

<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:

0.720

Hom.:

8791

Bravo

AF:

0.732

Asia WGS

AF:

0.783

AC:

2725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.69

(source)

DANN

Benign

0.51

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over