chr2-71124482-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_032601.4(MCEE):c.102C>T(p.Pro34Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,836 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
MCEE
NM_032601.4 synonymous
NM_032601.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.470
Genes affected
MCEE (HGNC:16732): (methylmalonyl-CoA epimerase) The product of this gene catalyzes the interconversion of D- and L-methylmalonyl-CoA during the degradation of branched chain amino acids. odd chain-length fatty acids, and other metabolites. Mutations in this gene result in methylmalonyl-CoA epimerase deficiency, which is presented as mild to moderate methylmalonic aciduria. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
Synonymous conserved (PhyloP=0.47 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MCEE | NM_032601.4 | c.102C>T | p.Pro34Pro | synonymous_variant | 2/3 | ENST00000244217.6 | NP_115990.3 | |
| MCEE | XM_047446039.1 | c.102C>T | p.Pro34Pro | synonymous_variant | 2/3 | XP_047301995.1 | ||
| MCEE | XM_005264613.3 | c.102C>T | p.Pro34Pro | synonymous_variant | 2/3 | XP_005264670.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MCEE | ENST00000244217.6 | c.102C>T | p.Pro34Pro | synonymous_variant | 2/3 | 1 | NM_032601.4 | ENSP00000244217.5 | ||
| MCEE | ENST00000486135.1 | c.-184C>T | 5_prime_UTR_variant | 3/3 | 3 | ENSP00000441569.1 | ||||
| MCEE | ENST00000494660.6 | c.-184C>T | 5_prime_UTR_variant | 2/2 | 2 | ENSP00000437361.1 | ||||
| MCEE | ENST00000413592.5 | c.-31C>T | upstream_gene_variant | 2 | ENSP00000391140.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250870Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135716
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461836Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727212
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GnomAD4 genome
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33
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at