chr12-53939186-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017410.3(HOXC13):c.280A>G(p.Thr94Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000749 in 1,521,474 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T94K) has been classified as Benign.
Frequency
Consequence
NM_017410.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXC13 | NM_017410.3 | c.280A>G | p.Thr94Ala | missense_variant | 1/2 | ENST00000243056.5 | |
HOXC13-AS | NR_047507.1 | n.173+285T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXC13 | ENST00000243056.5 | c.280A>G | p.Thr94Ala | missense_variant | 1/2 | 1 | NM_017410.3 | P1 | |
HOXC13-AS | ENST00000512916.2 | n.173+285T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 151664Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000424 AC: 5AN: 117818Hom.: 0 AF XY: 0.0000153 AC XY: 1AN XY: 65298
GnomAD4 exome AF: 0.0000694 AC: 95AN: 1369696Hom.: 0 Cov.: 33 AF XY: 0.0000622 AC XY: 42AN XY: 675530
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 151778Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74196
ClinVar
Submissions by phenotype
HOXC13-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 11, 2024 | The HOXC13 c.280A>G variant is predicted to result in the amino acid substitution p.Thr94Ala. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0090% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at