chr8-30132393-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP7
The NM_001100916.2(MBOAT4):āc.858C>Gā(p.Pro286Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000357 in 1,399,410 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.0000036 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MBOAT4
NM_001100916.2 synonymous
NM_001100916.2 synonymous
Scores
1
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.62
Genes affected
MBOAT4 (HGNC:32311): (membrane bound O-acyltransferase domain containing 4) Enables serine O-acyltransferase activity. Involved in peptidyl-serine octanoylation. Predicted to be located in endoplasmic reticulum. Predicted to be active in membrane. Predicted to be integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
LEPROTL1 (HGNC:6555): (leptin receptor overlapping transcript like 1) Enables identical protein binding activity. Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway and negative regulation of growth hormone receptor signaling pathway. Predicted to be integral component of membrane. Predicted to be active in endosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP7
Synonymous conserved (PhyloP=-2.62 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBOAT4 | ENST00000320542.4 | c.858C>G | p.Pro286Pro | synonymous_variant | Exon 3 of 3 | 1 | NM_001100916.2 | ENSP00000314196.3 | ||
LEPROTL1 | ENST00000442880.6 | c.298G>C | p.Gly100Arg | missense_variant | Exon 4 of 5 | 2 | ENSP00000412803.2 | |||
LEPROTL1 | ENST00000523116.5 | c.280-4879G>C | intron_variant | Intron 3 of 3 | 2 | ENSP00000428281.1 | ||||
LEPROTL1 | ENST00000520739.5 | n.279+27907G>C | intron_variant | Intron 3 of 5 | 4 | ENSP00000429398.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 152138Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 genomes
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32
FAILED QC
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GnomAD4 exome AF: 0.00000357 AC: 5AN: 1399410Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 690214
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74316
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MutPred
Gain of MoRF binding (P = 0.0217);
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at