chr10-12069074-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_018706.7(DHTKD1):c.41G>C(p.Gly14Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,460,644 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. G14R) has been classified as Uncertain significance.
Frequency
Consequence
NM_018706.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHTKD1 | NM_018706.7 | c.41G>C | p.Gly14Ala | missense_variant | 1/17 | ENST00000263035.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHTKD1 | ENST00000263035.9 | c.41G>C | p.Gly14Ala | missense_variant | 1/17 | 1 | NM_018706.7 | P1 | |
DHTKD1 | ENST00000437298.1 | c.41G>C | p.Gly14Ala | missense_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000815 AC: 2AN: 245410Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133990
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460644Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726674
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
2-aminoadipic 2-oxoadipic aciduria Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 21, 2023 | ClinVar contains an entry for this variant (Variation ID: 1949907). This variant has not been reported in the literature in individuals affected with DHTKD1-related conditions. This variant is present in population databases (rs747408194, gnomAD 0.01%). This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 14 of the DHTKD1 protein (p.Gly14Ala). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at