7-44624350-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002541.4(OGDH):c.7C>T(p.His3Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,130,772 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H3R) has been classified as Uncertain significance.
Frequency
Consequence
NM_002541.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00205 AC: 156AN: 75944Hom.: 0 Cov.: 18
GnomAD3 exomes AF: 0.000888 AC: 182AN: 204926Hom.: 1 AF XY: 0.000872 AC XY: 98AN XY: 112398
GnomAD4 exome AF: 0.00244 AC: 2573AN: 1054798Hom.: 5 Cov.: 36 AF XY: 0.00249 AC XY: 1278AN XY: 512392
GnomAD4 genome AF: 0.00205 AC: 156AN: 75974Hom.: 0 Cov.: 18 AF XY: 0.00198 AC XY: 68AN XY: 34368
ClinVar
Submissions by phenotype
Oxoglutaricaciduria Uncertain:1
This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 3 of the OGDH protein (p.His3Tyr). This variant is present in population databases (rs113587743, gnomAD 0.2%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with OGDH-related conditions. ClinVar contains an entry for this variant (Variation ID: 1355335). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at