19-32974193-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_152266.5(FAAP24):c.377C>T(p.Ser126Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00594 in 1,613,312 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_152266.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAAP24 | NM_152266.5 | c.377C>T | p.Ser126Phe | missense_variant | Exon 4 of 5 | ENST00000588258.6 | NP_689479.1 | |
FAAP24 | NM_001300978.2 | c.92C>T | p.Ser31Phe | missense_variant | Exon 2 of 3 | NP_001287907.1 | ||
FAAP24 | XM_005259393.4 | c.248C>T | p.Ser83Phe | missense_variant | Exon 4 of 5 | XP_005259450.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00484 AC: 737AN: 152218Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00541 AC: 1353AN: 250188Hom.: 12 AF XY: 0.00537 AC XY: 727AN XY: 135278
GnomAD4 exome AF: 0.00605 AC: 8842AN: 1460976Hom.: 50 Cov.: 31 AF XY: 0.00606 AC XY: 4405AN XY: 726798
GnomAD4 genome AF: 0.00484 AC: 737AN: 152336Hom.: 4 Cov.: 33 AF XY: 0.00448 AC XY: 334AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
FAAP24-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at