chr16-86578772-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005250.3(FOXL1):c.49A>T(p.Met17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,611,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005250.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXL1 | NM_005250.3 | c.49A>T | p.Met17Leu | missense_variant | 1/1 | ENST00000320241.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXL1 | ENST00000320241.5 | c.49A>T | p.Met17Leu | missense_variant | 1/1 | NM_005250.3 | P1 | ||
FOXL1 | ENST00000593625.1 | c.49A>T | p.Met17Leu | missense_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247898Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134582
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459758Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725978
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 19, 2022 | The c.49A>T (p.M17L) alteration is located in exon 1 (coding exon 1) of the FOXL1 gene. This alteration results from a A to T substitution at nucleotide position 49, causing the methionine (M) at amino acid position 17 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