rs3740094
Positions:
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.Leu54=) 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
NM_007021.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.247
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]
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]
Genome browser will be placed here
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 | UniProt |
---|---|---|---|---|---|---|---|
DEPP1 | NM_007021.4 | c.162G>A | p.Leu54= | synonymous_variant | 2/2 | ENST00000298295.4 | |
RASSF4 | NM_032023.4 | c.139-4652C>T | intron_variant | ENST00000340258.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEPP1 | ENST00000298295.4 | c.162G>A | p.Leu54= | synonymous_variant | 2/2 | 1 | NM_007021.4 | P1 | |
RASSF4 | ENST00000340258.10 | c.139-4652C>T | intron_variant | 1 | NM_032023.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.127 AC: 19354AN: 152152Hom.: 1546 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
19354
AN:
152152
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.159 AC: 39538AN: 248230Hom.: 3579 AF XY: 0.165 AC XY: 22167AN XY: 134748
GnomAD3 exomes
AF:
AC:
39538
AN:
248230
Hom.:
AF XY:
AC XY:
22167
AN XY:
134748
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.158 AC: 230909AN: 1458938Hom.: 19473 Cov.: 33 AF XY: 0.160 AC XY: 116193AN XY: 725606
GnomAD4 exome
AF:
AC:
230909
AN:
1458938
Hom.:
Cov.:
33
AF XY:
AC XY:
116193
AN XY:
725606
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.127 AC: 19373AN: 152270Hom.: 1556 Cov.: 33 AF XY: 0.129 AC XY: 9592AN XY: 74444
GnomAD4 genome
?
AF:
AC:
19373
AN:
152270
Hom.:
Cov.:
33
AF XY:
AC XY:
9592
AN XY:
74444
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
937
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at