chr16-86579232-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005250.3(FOXL1):c.509C>A(p.Pro170Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000523 in 1,529,218 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P170L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005250.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXL1 | NM_005250.3 | c.509C>A | p.Pro170Gln | missense_variant | 1/1 | ENST00000320241.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXL1 | ENST00000320241.5 | c.509C>A | p.Pro170Gln | missense_variant | 1/1 | NM_005250.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151904Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000478 AC: 6AN: 125414Hom.: 0 AF XY: 0.0000146 AC XY: 1AN XY: 68724
GnomAD4 exome AF: 0.00000436 AC: 6AN: 1377206Hom.: 0 Cov.: 29 AF XY: 0.00000294 AC XY: 2AN XY: 679182
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152012Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.509C>A (p.P170Q) alteration is located in exon 1 (coding exon 1) of the FOXL1 gene. This alteration results from a C to A substitution at nucleotide position 509, causing the proline (P) at amino acid position 170 to be replaced by a glutamine (Q). 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