chr4-145619443-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_172250.3(MMAA):c.-66+36G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00732 in 152,336 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0073 ( 12 hom., cov: 32)
Exomes 𝑓: 0.027 ( 0 hom. )
Consequence
MMAA
NM_172250.3 intron
NM_172250.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.60
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=-0.81).
BP6
?
Variant 4-145619443-G-C is Benign according to our data. Variant chr4-145619443-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1326747.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (SAS) allele frequency = 0.0714 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMAA | NM_172250.3 | c.-66+36G>C | intron_variant | ENST00000649156.2 | |||
MMAA | NM_001375644.1 | c.-272G>C | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMAA | ENST00000649156.2 | c.-66+36G>C | intron_variant | NM_172250.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00732 AC: 1113AN: 152144Hom.: 12 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.0270 AC: 2AN: 74Hom.: 0 Cov.: 0 AF XY: 0.0200 AC XY: 1AN XY: 50
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GnomAD4 genome ? AF: 0.00731 AC: 1113AN: 152262Hom.: 12 Cov.: 32 AF XY: 0.00721 AC XY: 537AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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