chr7-76048186-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005918.4(MDH2):c.26C>T(p.Ala9Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 1,536,850 control chromosomes in the GnomAD database, including 98,394 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. A9A) has been classified as Likely benign.
Frequency
Consequence
NM_005918.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MDH2 | NM_005918.4 | c.26C>T | p.Ala9Val | missense_variant | 1/9 | ENST00000315758.10 | |
MDH2 | NM_001282403.2 | c.26C>T | p.Ala9Val | missense_variant | 1/8 | ||
MDH2 | NM_001282404.2 | c.-127C>T | 5_prime_UTR_variant | 1/8 | |||
MDH2 | NR_104165.2 | n.81C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MDH2 | ENST00000315758.10 | c.26C>T | p.Ala9Val | missense_variant | 1/9 | 1 | NM_005918.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.430 AC: 65360AN: 152050Hom.: 15706 Cov.: 35
GnomAD3 exomes AF: 0.401 AC: 56807AN: 141784Hom.: 12483 AF XY: 0.395 AC XY: 30178AN XY: 76476
GnomAD4 exome AF: 0.333 AC: 461617AN: 1384682Hom.: 82646 Cov.: 56 AF XY: 0.335 AC XY: 229237AN XY: 683570
GnomAD4 genome ? AF: 0.430 AC: 65459AN: 152168Hom.: 15748 Cov.: 35 AF XY: 0.439 AC XY: 32690AN XY: 74390
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at