chr22-43143107-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173467.5(MCAT):c.242T>G(p.Leu81Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000324 in 1,604,212 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as no classification for the single variant (no stars).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
MCAT
NM_173467.5 missense
NM_173467.5 missense
Scores
7
11
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.87
Genes affected
MCAT (HGNC:29622): (malonyl-CoA-acyl carrier protein transacylase) The protein encoded by this gene is found exclusively in the mitochondrion, where it catalyzes the transfer of a malonyl group from malonyl-CoA to the mitochondrial acyl carrier protein. The encoded protein may be part of a fatty acid synthase complex that is more like the type II prokaryotic and plastid complexes rather than the type I human cytosolic complex. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCAT | NM_173467.5 | c.242T>G | p.Leu81Arg | missense_variant | 1/4 | ENST00000290429.11 | |
MCAT | NM_014507.3 | c.242T>G | p.Leu81Arg | missense_variant | 1/3 | ||
MCAT | NR_046423.1 | n.291T>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCAT | ENST00000290429.11 | c.242T>G | p.Leu81Arg | missense_variant | 1/4 | 1 | NM_173467.5 | P1 | |
MCAT | ENST00000327555.5 | c.242T>G | p.Leu81Arg | missense_variant | 1/3 | 1 | |||
MCAT | ENST00000464244.1 | n.174T>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152236Hom.: 0 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000226 AC: 51AN: 226148Hom.: 0 AF XY: 0.000192 AC XY: 24AN XY: 125064
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GnomAD4 exome AF: 0.0000282 AC: 41AN: 1451858Hom.: 0 Cov.: 32 AF XY: 0.0000221 AC XY: 16AN XY: 722370
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GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74502
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T;T
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H;H
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Gain of methylation at L81 (P = 6e-04);Gain of methylation at L81 (P = 6e-04);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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