chr10-49736444-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_018245.3(OGDHL):c.2667C>T(p.Phe889=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00142 in 1,613,940 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0015 ( 2 hom. )
Consequence
OGDHL
NM_018245.3 synonymous
NM_018245.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.85
Genes affected
OGDHL (HGNC:25590): (oxoglutarate dehydrogenase L) The protein encoded by this gene is similar to oxoglutarate dehydrogenase (OGDH) of the OGDH complex, which degrades glucose and glutamate. This gene encodes several isoforms, including some that appear to localize to mitochondria. The encoded protein down-regulates the AKT signaling cascade and can suppress the growth of cervical cancer cells. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 10-49736444-G-A is Benign according to our data. Variant chr10-49736444-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 710350.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OGDHL | NM_018245.3 | c.2667C>T | p.Phe889= | synonymous_variant | 21/23 | ENST00000374103.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OGDHL | ENST00000374103.9 | c.2667C>T | p.Phe889= | synonymous_variant | 21/23 | 1 | NM_018245.3 | P1 | |
OGDHL | ENST00000419399.4 | c.2496C>T | p.Phe832= | synonymous_variant | 20/22 | 2 | |||
OGDHL | ENST00000432695.2 | c.2040C>T | p.Phe680= | synonymous_variant | 19/21 | 2 | |||
OGDHL | ENST00000490844.1 | n.1703C>T | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000920 AC: 140AN: 152184Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000840 AC: 211AN: 251286Hom.: 1 AF XY: 0.000766 AC XY: 104AN XY: 135830
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GnomAD4 exome AF: 0.00147 AC: 2151AN: 1461756Hom.: 2 Cov.: 34 AF XY: 0.00148 AC XY: 1075AN XY: 727190
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
OGDHL-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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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