17-41813049-C-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_021939.4(FKBP10):c.15C>A(p.Gly5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000833 in 1,609,286 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G5G) has been classified as Likely benign.
Frequency
Consequence
NM_021939.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKBP10 | NM_021939.4 | c.15C>A | p.Gly5= | synonymous_variant | 1/10 | ENST00000321562.9 | |
FKBP10 | XM_011525099.4 | c.15C>A | p.Gly5= | synonymous_variant | 1/11 | ||
FKBP10 | XM_011525100.3 | c.-113C>A | 5_prime_UTR_variant | 1/10 | |||
FKBP10 | XM_047436515.1 | c.-113C>A | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKBP10 | ENST00000321562.9 | c.15C>A | p.Gly5= | synonymous_variant | 1/10 | 1 | NM_021939.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000220 AC: 52AN: 236734Hom.: 0 AF XY: 0.000268 AC XY: 35AN XY: 130532
GnomAD4 exome AF: 0.0000899 AC: 131AN: 1457094Hom.: 1 Cov.: 31 AF XY: 0.000134 AC XY: 97AN XY: 724820
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 08, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at