rs2841280
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138790.5(PLD4):c.79G>A(p.Glu27Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PLD4
NM_138790.5 missense
NM_138790.5 missense
Scores
19
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.22
Publications
32 publications found
Genes affected
PLD4 (HGNC:23792): (phospholipase D family member 4) Predicted to enable single-stranded DNA 5'-3' exodeoxyribonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. Predicted to be located in early endosome and endoplasmic reticulum membrane. Predicted to be active in several cellular components, including endoplasmic reticulum; phagocytic vesicle; and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.042895406).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PLD4 | NM_138790.5 | c.79G>A | p.Glu27Lys | missense_variant | Exon 2 of 11 | ENST00000392593.9 | NP_620145.2 | |
| PLD4 | NM_001308174.2 | c.100G>A | p.Glu34Lys | missense_variant | Exon 2 of 11 | NP_001295103.1 | ||
| PLD4 | XM_011536411.3 | c.100G>A | p.Glu34Lys | missense_variant | Exon 2 of 11 | XP_011534713.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1398638Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 690444
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1398638
Hom.:
Cov.:
37
AF XY:
AC XY:
0
AN XY:
690444
African (AFR)
AF:
AC:
0
AN:
31792
American (AMR)
AF:
AC:
0
AN:
35046
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24964
East Asian (EAS)
AF:
AC:
0
AN:
36192
South Asian (SAS)
AF:
AC:
0
AN:
79108
European-Finnish (FIN)
AF:
AC:
0
AN:
48360
Middle Eastern (MID)
AF:
AC:
0
AN:
5628
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1079692
Other (OTH)
AF:
AC:
0
AN:
57856
GnomAD4 genome
GnomAD4 genome
Cov.:
33
TwinsUK
AF:
AC:
1
ALSPAC
AF:
AC:
0
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
.;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;N;.
PhyloP100
PrimateAI
Benign
T
PROVEAN
Benign
.;N;N;N
REVEL
Benign
Sift
Benign
.;T;T;T
Sift4G
Benign
.;T;T;T
Polyphen
0.0
.;B;B;.
Vest4
0.089, 0.088
MutPred
0.37
.;Gain of catalytic residue at Q39 (P = 0.0077);.;.;
MVP
0.18
MPC
0.096
ClinPred
T
GERP RS
Varity_R
gMVP
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
Publications
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