rs10513187
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015258.2(FKBP15):c.*3426G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 1,126,300 control chromosomes in the GnomAD database, including 601 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.036 ( 137 hom., cov: 31)
Exomes 𝑓: 0.027 ( 464 hom. )
Consequence
FKBP15
NM_015258.2 3_prime_UTR
NM_015258.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.137
Genes affected
FKBP15 (HGNC:23397): (FKBP prolyl isomerase family member 15) Predicted to enable actin binding activity and peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in endocytosis and protein peptidyl-prolyl isomerization. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
SLC31A2 (HGNC:11017): (solute carrier family 31 member 2) Predicted to enable copper ion transmembrane transporter activity. Predicted to be involved in cellular copper ion homeostasis. Predicted to act upstream of or within regulation of copper ion transmembrane transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0574 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKBP15 | NM_015258.2 | c.*3426G>C | 3_prime_UTR_variant | 28/28 | ENST00000238256.8 | ||
SLC31A2 | NM_001860.3 | c.264-97C>G | intron_variant | ENST00000259392.8 | |||
FKBP15 | XM_006717018.3 | c.*3426G>C | 3_prime_UTR_variant | 28/28 | |||
FKBP15 | XM_006717019.2 | c.*3426G>C | 3_prime_UTR_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKBP15 | ENST00000238256.8 | c.*3426G>C | 3_prime_UTR_variant | 28/28 | 1 | NM_015258.2 | P2 | ||
SLC31A2 | ENST00000259392.8 | c.264-97C>G | intron_variant | 1 | NM_001860.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0362 AC: 5505AN: 152022Hom.: 137 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
5505
AN:
152022
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0273 AC: 26583AN: 974160Hom.: 464 Cov.: 12 AF XY: 0.0273 AC XY: 13455AN XY: 493046
GnomAD4 exome
AF:
AC:
26583
AN:
974160
Hom.:
Cov.:
12
AF XY:
AC XY:
13455
AN XY:
493046
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0362 AC: 5513AN: 152140Hom.: 137 Cov.: 31 AF XY: 0.0345 AC XY: 2563AN XY: 74370
GnomAD4 genome
?
AF:
AC:
5513
AN:
152140
Hom.:
Cov.:
31
AF XY:
AC XY:
2563
AN XY:
74370
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
44
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at