16-86567489-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005251.3(FOXC2):āc.154A>Gā(p.Met52Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005251.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXC2 | NM_005251.3 | c.154A>G | p.Met52Val | missense_variant | 1/1 | ENST00000649859.1 | NP_005242.1 | |
FOXC2-AS1 | NR_125795.1 | n.145+128T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXC2 | ENST00000649859.1 | c.154A>G | p.Met52Val | missense_variant | 1/1 | NM_005251.3 | ENSP00000497759.1 | |||
FOXC2-AS1 | ENST00000563280.3 | n.231+128T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151980Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250766Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135718
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461496Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727080
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.154A>G (p.M52V) alteration is located in exon 1 (coding exon 1) of the FOXC2 gene. This alteration results from a A to G substitution at nucleotide position 154, causing the methionine (M) at amino acid position 52 to be replaced by a valine (V). 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