12-53973307-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014212.4(HOXC11):c.66C>G(p.Phe22Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014212.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXC11 | ENST00000546378.1 | c.66C>G | p.Phe22Leu | missense_variant | Exon 1 of 2 | 1 | NM_014212.4 | ENSP00000446680.1 | ||
HOXC11 | ENST00000243082.4 | c.66C>G | p.Phe22Leu | missense_variant | Exon 1 of 2 | 3 | ENSP00000243082.4 | |||
HOTAIR | ENST00000424518.5 | n.59+1591G>C | intron_variant | Intron 1 of 6 | 5 | |||||
HOTAIR | ENST00000455246.6 | n.59+1591G>C | intron_variant | Intron 1 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251012Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135718
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461688Hom.: 0 Cov.: 40 AF XY: 0.00000688 AC XY: 5AN XY: 727166
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.66C>G (p.F22L) alteration is located in exon 1 (coding exon 1) of the HOXC11 gene. This alteration results from a C to G substitution at nucleotide position 66, causing the phenylalanine (F) at amino acid position 22 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at