chr8-30132393-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP7

The NM_001100916.2(MBOAT4):ā€‹c.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

Scores

1
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.62
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MBOAT4NM_001100916.2 linkc.858C>G p.Pro286Pro synonymous_variant Exon 3 of 3 ENST00000320542.4 NP_001094386.1 Q96T53-1
LEPROTL1NM_001128208.2 linkc.280-4879G>C intron_variant Intron 3 of 3 NP_001121680.1 O95214-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MBOAT4ENST00000320542.4 linkc.858C>G p.Pro286Pro synonymous_variant Exon 3 of 3 1 NM_001100916.2 ENSP00000314196.3 Q96T53-1
LEPROTL1ENST00000442880.6 linkc.298G>C p.Gly100Arg missense_variant Exon 4 of 5 2 ENSP00000412803.2 C9JVM4
LEPROTL1ENST00000523116.5 linkc.280-4879G>C intron_variant Intron 3 of 3 2 ENSP00000428281.1 O95214-2
LEPROTL1ENST00000520739.5 linkn.279+27907G>C intron_variant Intron 3 of 5 4 ENSP00000429398.1 E5RIL0

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
2
AN:
152138
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000357
AC:
5
AN:
1399410
Hom.:
0
Cov.:
34
AF XY:
0.00
AC XY:
0
AN XY:
690214
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000463
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000131
AC:
2
AN:
152138
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.52
T
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.020
DANN
Benign
0.36
DEOGEN2
Benign
0.092
T
Eigen
Benign
-1.7
Eigen_PC
Benign
-1.9
FATHMM_MKL
Benign
0.020
N
LIST_S2
Benign
0.42
T
M_CAP
Benign
0.0025
T
MetaRNN
Uncertain
0.49
T
MetaSVM
Benign
-0.96
T
PROVEAN
Benign
-2.0
N
REVEL
Benign
0.097
Sift
Benign
0.14
T
Sift4G
Benign
0.37
T
Vest4
0.22
MutPred
0.85
Gain of MoRF binding (P = 0.0217);
MVP
0.068
ClinPred
0.079
T
GERP RS
-10
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs16876562; hg19: chr8-29989909; API