2-206755291-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001039845.3(MDH1B):c.628G>A(p.Val210Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000214 in 1,614,192 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039845.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MDH1B | NM_001039845.3 | c.628G>A | p.Val210Ile | missense_variant | 5/12 | ENST00000374412.8 | NP_001034934.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MDH1B | ENST00000374412.8 | c.628G>A | p.Val210Ile | missense_variant | 5/12 | 1 | NM_001039845.3 | ENSP00000363533 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251066Hom.: 1 AF XY: 0.000184 AC XY: 25AN XY: 135686
GnomAD4 exome AF: 0.000224 AC: 327AN: 1461872Hom.: 3 Cov.: 31 AF XY: 0.000232 AC XY: 169AN XY: 727240
GnomAD4 genome AF: 0.000118 AC: 18AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.628G>A (p.V210I) alteration is located in exon 5 (coding exon 5) of the MDH1B gene. This alteration results from a G to A substitution at nucleotide position 628, causing the valine (V) at amino acid position 210 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at