chr4-145619459-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_172250.3(MMAA):c.-66+52C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,320 control chromosomes in the GnomAD database, including 554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.075 ( 553 hom., cov: 32)
Exomes 𝑓: 0.073 ( 1 hom. )
Consequence
MMAA
NM_172250.3 intron
NM_172250.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0120
Genes affected
MMAA (HGNC:18871): (metabolism of cobalamin associated A) The protein encoded by this gene is involved in the translocation of cobalamin into the mitochondrion, where it is used in the final steps of adenosylcobalamin synthesis. Adenosylcobalamin is a coenzyme required for the activity of methylmalonyl-CoA mutase. Defects in this gene are a cause of methylmalonic aciduria. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 4-145619459-C-T is Benign according to our data. Variant chr4-145619459-C-T is described in ClinVar as [Benign]. Clinvar id is 1240548.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMAA | NM_172250.3 | c.-66+52C>T | intron_variant | ENST00000649156.2 | |||
MMAA | NM_001375644.1 | c.-256C>T | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMAA | ENST00000649156.2 | c.-66+52C>T | intron_variant | NM_172250.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0751 AC: 11429AN: 152092Hom.: 555 Cov.: 32
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GnomAD4 exome AF: 0.0727 AC: 8AN: 110Hom.: 1 AF XY: 0.0854 AC XY: 7AN XY: 82
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GnomAD4 genome ? AF: 0.0751 AC: 11436AN: 152210Hom.: 553 Cov.: 32 AF XY: 0.0758 AC XY: 5641AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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