Variant rs3740094 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007021.4(DEPP1):c.162G>A(p.Leu54Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,611,208 control chromosomes in the GnomAD database, including 21,029 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 0.13 ( 1556 hom., cov: 33)

Exomes 𝑓: 0.16 ( 19473 hom. )

Consequence

DEPP1
NM_007021.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.247

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:

RASSF4 (HGNC:):

RASSF4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP7

Synonymous conserved (PhyloP=-0.247 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEPP1	NM_007021.4 linkuse as main transcript	c.162G>A	p.Leu54Leu	synonymous_variant	2/2	ENST00000298295.4	NP_008952.1	Q9NTK1
RASSF4	NM_032023.4 linkuse as main transcript	c.139-4652C>T		intron_variant		ENST00000340258.10	NP_114412.2	Q9H2L5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEPP1	ENST00000298295.4 linkuse as main transcript	c.162G>A	p.Leu54Leu	synonymous_variant	2/2	1	NM_007021.4	ENSP00000298295.3		Q9NTK1
RASSF4	ENST00000340258.10 linkuse as main transcript	c.139-4652C>T		intron_variant		1	NM_032023.4	ENSP00000339692.4		Q9H2L5-1

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19354

AN:

152152

Hom.:

1546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0337

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.152

GnomAD3 exomes

AF:

0.159

AC:

39538

AN:

248230

Hom.:

3579

AF XY:

0.165

AC XY:

22167

AN XY:

134748

show subpopulations

Gnomad AFR exome

AF:

0.0320

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.286

Gnomad SAS exome

AF:

0.193

Gnomad FIN exome

AF:

0.159

Gnomad NFE exome

AF:

0.164

Gnomad OTH exome

AF:

0.171

GnomAD4 exome

AF:

0.158

AC:

230909

AN:

1458938

Hom.:

19473

Cov.:

AF XY:

0.160

AC XY:

116193

AN XY:

725606

show subpopulations

Gnomad4 AFR exome

AF:

0.0278

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.319

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.160

Gnomad4 NFE exome

AF:

0.156

Gnomad4 OTH exome

AF:

0.161

GnomAD4 genome

AF:

0.127

AC:

19373

AN:

152270

Hom.:

1556

Cov.:

AF XY:

0.129

AC XY:

9592

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0336

Gnomad4 AMR

AF:

0.113

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.298

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.161

Alfa

AF:

0.154

Hom.:

2552

Bravo

AF:

0.121

Asia WGS

AF:

0.270

AC:

937

AN:

3478

EpiCase

AF:

0.166

EpiControl

AF:

0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.8

DANN

Benign

0.70

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over