chr3-138947449-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001040061.3(FOXL2NB):āc.85T>Gā(p.Ser29Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000725 in 1,516,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001040061.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXL2NB | NM_001040061.3 | c.85T>G | p.Ser29Ala | missense_variant | 1/3 | ENST00000383165.4 | NP_001035150.1 | |
FOXL2NB | XM_005247443.4 | c.-76T>G | 5_prime_UTR_variant | 1/4 | XP_005247500.1 | |||
FOXL2NB | XM_024453517.2 | c.-175T>G | 5_prime_UTR_variant | 1/2 | XP_024309285.1 | |||
FOXL2NB | XM_024453518.2 | c.-258T>G | 5_prime_UTR_variant | 1/3 | XP_024309286.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXL2NB | ENST00000383165.4 | c.85T>G | p.Ser29Ala | missense_variant | 1/3 | 2 | NM_001040061.3 | ENSP00000372651 | P1 | |
FOXL2NB | ENST00000470680.5 | c.85T>G | p.Ser29Ala | missense_variant, NMD_transcript_variant | 1/3 | 3 | ENSP00000418272 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151404Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000147 AC: 2AN: 1364926Hom.: 0 Cov.: 32 AF XY: 0.00000149 AC XY: 1AN XY: 672410
GnomAD4 genome AF: 0.0000594 AC: 9AN: 151540Hom.: 0 Cov.: 32 AF XY: 0.0000810 AC XY: 6AN XY: 74098
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.85T>G (p.S29A) alteration is located in exon 1 (coding exon 1) of the FOXL2NB gene. This alteration results from a T to G substitution at nucleotide position 85, causing the serine (S) at amino acid position 29 to be replaced by an alanine (A). 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