12-53939166-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017410.3(HOXC13):c.260C>T(p.Ala87Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,485,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017410.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000739 AC: 6AN: 81232Hom.: 0 AF XY: 0.0000431 AC XY: 2AN XY: 46444
GnomAD4 exome AF: 0.0000120 AC: 16AN: 1333558Hom.: 0 Cov.: 33 AF XY: 0.00000913 AC XY: 6AN XY: 657118
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74256
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at