chr17-41813055-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS1
The NM_021939.4(FKBP10):c.21C>T(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000189 in 1,610,298 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P7P) 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKBP10 | NM_021939.4 | c.21C>T | p.Pro7= | synonymous_variant | 1/10 | ENST00000321562.9 | |
FKBP10 | XM_011525099.4 | c.21C>T | p.Pro7= | synonymous_variant | 1/11 | ||
FKBP10 | XM_011525100.3 | c.-107C>T | 5_prime_UTR_variant | 1/10 | |||
FKBP10 | XM_047436515.1 | c.-107C>T | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKBP10 | ENST00000321562.9 | c.21C>T | p.Pro7= | synonymous_variant | 1/10 | 1 | NM_021939.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000293 AC: 70AN: 239160Hom.: 0 AF XY: 0.000296 AC XY: 39AN XY: 131646
GnomAD4 exome AF: 0.000193 AC: 282AN: 1457988Hom.: 4 Cov.: 31 AF XY: 0.000215 AC XY: 156AN XY: 725266
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74476
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | FKBP10: BP4 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 21, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 15, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Osteogenesis imperfecta type 11 Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Medical Molecular Genetics Department, National Research Center | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at