3-138950555-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040061.3(FOXL2NB):c.511C>T(p.Leu171Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040061.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXL2NB | NM_001040061.3 | c.511C>T | p.Leu171Phe | missense_variant | 3/3 | ENST00000383165.4 | NP_001035150.1 | |
FOXL2NB | XM_005247443.4 | c.442C>T | p.Leu148Phe | missense_variant | 4/4 | XP_005247500.1 | ||
FOXL2NB | XM_024453517.2 | c.*312C>T | 3_prime_UTR_variant | 2/2 | XP_024309285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXL2NB | ENST00000383165.4 | c.511C>T | p.Leu171Phe | missense_variant | 3/3 | 2 | NM_001040061.3 | ENSP00000372651 | P1 | |
FOXL2NB | ENST00000498709.1 | n.1440C>T | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
FOXL2NB | ENST00000470680.5 | c.*393C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 3 | ENSP00000418272 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249542Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135392
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 23, 2024 | The c.511C>T (p.L171F) alteration is located in exon 3 (coding exon 3) of the FOXL2NB gene. This alteration results from a C to T substitution at nucleotide position 511, causing the leucine (L) at amino acid position 171 to be replaced by a phenylalanine (F). 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