7-30019098-C-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_017946.4(FKBP14):āc.375G>Cā(p.Leu125=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,581,300 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L125L) has been classified as Likely benign.
Frequency
Consequence
NM_017946.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKBP14 | NM_017946.4 | c.375G>C | p.Leu125= | synonymous_variant | 3/4 | ENST00000222803.10 | |
FKBP14 | XM_047420550.1 | c.375G>C | p.Leu125= | synonymous_variant | 3/4 | ||
FKBP14 | NR_046478.2 | n.661G>C | non_coding_transcript_exon_variant | 4/5 | |||
FKBP14 | NR_046479.2 | n.417G>C | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKBP14 | ENST00000222803.10 | c.375G>C | p.Leu125= | synonymous_variant | 3/4 | 1 | NM_017946.4 | P1 | |
FKBP14-AS1 | ENST00000422239.6 | n.680-6289C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 224AN: 152056Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00145 AC: 315AN: 217214Hom.: 4 AF XY: 0.00144 AC XY: 170AN XY: 118314
GnomAD4 exome AF: 0.00108 AC: 1546AN: 1429126Hom.: 5 Cov.: 31 AF XY: 0.00107 AC XY: 763AN XY: 710590
GnomAD4 genome AF: 0.00148 AC: 225AN: 152174Hom.: 2 Cov.: 33 AF XY: 0.00179 AC XY: 133AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 28, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | FKBP14: BP4, BS2 - |
Ehlers-Danlos syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jan 01, 2020 | - - |
Ehlers-Danlos syndrome, kyphoscoliotic type, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2019 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at