chr16-86579348-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005250.3(FOXL1):c.625C>T(p.Pro209Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000885 in 1,492,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXL1 | NM_005250.3 | c.625C>T | p.Pro209Ser | missense_variant | 1/1 | ENST00000320241.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXL1 | ENST00000320241.5 | c.625C>T | p.Pro209Ser | missense_variant | 1/1 | NM_005250.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000790 AC: 12AN: 151874Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000227 AC: 21AN: 92674Hom.: 0 AF XY: 0.000268 AC XY: 14AN XY: 52266
GnomAD4 exome AF: 0.0000895 AC: 120AN: 1340196Hom.: 0 Cov.: 35 AF XY: 0.0000923 AC XY: 61AN XY: 661166
GnomAD4 genome ? AF: 0.0000790 AC: 12AN: 151874Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74162
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.625C>T (p.P209S) alteration is located in exon 1 (coding exon 1) of the FOXL1 gene. This alteration results from a C to T substitution at nucleotide position 625, causing the proline (P) at amino acid position 209 to be replaced by a serine (S). 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