19-32973319-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152266.5(FAAP24):c.106+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,612,610 control chromosomes in the GnomAD database, including 26,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_152266.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAAP24 | NM_152266.5 | c.106+17C>T | intron_variant | Intron 2 of 4 | ENST00000588258.6 | NP_689479.1 | ||
FAAP24 | NM_001300978.2 | c.-42-741C>T | intron_variant | Intron 1 of 2 | NP_001287907.1 | |||
FAAP24 | XM_005259393.4 | c.35+17C>T | intron_variant | Intron 2 of 4 | XP_005259450.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.180 AC: 27325AN: 151916Hom.: 2745 Cov.: 32
GnomAD3 exomes AF: 0.147 AC: 36676AN: 250314Hom.: 3246 AF XY: 0.148 AC XY: 20031AN XY: 135340
GnomAD4 exome AF: 0.174 AC: 254310AN: 1460578Hom.: 23558 Cov.: 36 AF XY: 0.173 AC XY: 125737AN XY: 726516
GnomAD4 genome AF: 0.180 AC: 27355AN: 152032Hom.: 2751 Cov.: 32 AF XY: 0.175 AC XY: 13022AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 23% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at