chr12-53939187-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_017410.3(HOXC13):c.281C>A(p.Thr94Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00334 in 1,522,010 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T94A) has been classified as Uncertain significance.
Frequency
Consequence
NM_017410.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXC13 | NM_017410.3 | c.281C>A | p.Thr94Lys | missense_variant | 1/2 | ENST00000243056.5 | |
HOXC13-AS | NR_047507.1 | n.173+284G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXC13 | ENST00000243056.5 | c.281C>A | p.Thr94Lys | missense_variant | 1/2 | 1 | NM_017410.3 | P1 | |
HOXC13-AS | ENST00000512916.2 | n.173+284G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00256 AC: 390AN: 152132Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00392 AC: 461AN: 117550Hom.: 3 AF XY: 0.00438 AC XY: 285AN XY: 65134
GnomAD4 exome AF: 0.00342 AC: 4689AN: 1369764Hom.: 16 Cov.: 33 AF XY: 0.00353 AC XY: 2386AN XY: 675528
GnomAD4 genome ? AF: 0.00257 AC: 391AN: 152246Hom.: 3 Cov.: 32 AF XY: 0.00265 AC XY: 197AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at