12-54054322-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_153633.3(HOXC4):āc.400A>Gā(p.Ile134Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,567,228 control chromosomes in the GnomAD database, including 24,934 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_153633.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HOXC4 | NM_153633.3 | c.400A>G | p.Ile134Val | missense_variant | 1/2 | ENST00000430889.3 | NP_705897.1 | |
HOXC4 | NM_014620.6 | c.400A>G | p.Ile134Val | missense_variant | 3/4 | NP_055435.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.137 AC: 19461AN: 142272Hom.: 1595 Cov.: 28
GnomAD3 exomes AF: 0.153 AC: 36106AN: 236348Hom.: 3298 AF XY: 0.163 AC XY: 21072AN XY: 129418
GnomAD4 exome AF: 0.176 AC: 250884AN: 1424876Hom.: 23333 Cov.: 35 AF XY: 0.179 AC XY: 126595AN XY: 708514
GnomAD4 genome AF: 0.137 AC: 19485AN: 142352Hom.: 1601 Cov.: 28 AF XY: 0.137 AC XY: 9481AN XY: 69136
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at