2-71109848-TCA-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_032601.4(MCEE):c.*120_*121delTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 781,070 control chromosomes in the GnomAD database, including 571 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.041 ( 378 hom., cov: 30)
Exomes 𝑓: 0.0078 ( 193 hom. )
Consequence
MCEE
NM_032601.4 3_prime_UTR
NM_032601.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.119
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 was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP6
Variant 2-71109848-TCA-T is Benign according to our data. Variant chr2-71109848-TCA-T is described in ClinVar as [Likely_benign]. Clinvar id is 336934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCEE | ENST00000244217 | c.*120_*121delTG | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_032601.4 | ENSP00000244217.5 | |||
MCEE | ENST00000413592 | c.*120_*121delTG | 3_prime_UTR_variant | Exon 2 of 2 | 2 | ENSP00000391140.1 | ||||
MCEE | ENST00000462609.2 | n.597_598delTG | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0407 AC: 6185AN: 152122Hom.: 376 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
6185
AN:
152122
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00778 AC: 4890AN: 628830Hom.: 193 AF XY: 0.00725 AC XY: 2417AN XY: 333338 show subpopulations
GnomAD4 exome
AF:
AC:
4890
AN:
628830
Hom.:
AF XY:
AC XY:
2417
AN XY:
333338
Gnomad4 AFR exome
AF:
AC:
2182
AN:
16242
Gnomad4 AMR exome
AF:
AC:
259
AN:
28222
Gnomad4 ASJ exome
AF:
AC:
23
AN:
19092
Gnomad4 EAS exome
AF:
AC:
183
AN:
32298
Gnomad4 SAS exome
AF:
AC:
687
AN:
56212
Gnomad4 FIN exome
AF:
AC:
3
AN:
34954
Gnomad4 NFE exome
AF:
AC:
992
AN:
406538
Gnomad4 Remaining exome
AF:
AC:
515
AN:
32152
Heterozygous variant carriers
0
213
426
639
852
1065
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
58
116
174
232
290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0406 AC: 6188AN: 152240Hom.: 378 Cov.: 30 AF XY: 0.0388 AC XY: 2890AN XY: 74456 show subpopulations
GnomAD4 genome
AF:
AC:
6188
AN:
152240
Hom.:
Cov.:
30
AF XY:
AC XY:
2890
AN XY:
74456
Gnomad4 AFR
AF:
AC:
0.134048
AN:
0.134048
Gnomad4 AMR
AF:
AC:
0.0168649
AN:
0.0168649
Gnomad4 ASJ
AF:
AC:
0.000576369
AN:
0.000576369
Gnomad4 EAS
AF:
AC:
0.0098228
AN:
0.0098228
Gnomad4 SAS
AF:
AC:
0.0122153
AN:
0.0122153
Gnomad4 FIN
AF:
AC:
0
AN:
0
Gnomad4 NFE
AF:
AC:
0.00274976
AN:
0.00274976
Gnomad4 OTH
AF:
AC:
0.0279092
AN:
0.0279092
Heterozygous variant carriers
0
275
550
824
1099
1374
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
62
124
186
248
310
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
52
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 16, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Methylmalonic acidemia Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mutation Taster
=100/0
polymorphism (auto)
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