rs10517743
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020116.5(FSTL5):c.1842-533C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 153,954 control chromosomes in the GnomAD database, including 326 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 0.040 ( 320 hom., cov: 33)
Exomes 𝑓: 0.057 ( 6 hom. )
Consequence
FSTL5
NM_020116.5 intron
NM_020116.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.126
Genes affected
FSTL5 (HGNC:21386): (follistatin like 5) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be located in extracellular region. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FSTL5 | NM_020116.5 | c.1842-533C>G | intron_variant | ENST00000306100.10 | |||
FSTL5 | NM_001128427.3 | c.1839-533C>G | intron_variant | ||||
FSTL5 | NM_001128428.3 | c.1812-533C>G | intron_variant | ||||
FSTL5 | XM_011532126.1 | c.1815-533C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FSTL5 | ENST00000306100.10 | c.1842-533C>G | intron_variant | 1 | NM_020116.5 | P5 | |||
FSTL5 | ENST00000379164.8 | c.1839-533C>G | intron_variant | 1 | A1 | ||||
FSTL5 | ENST00000427802.2 | c.1812-533C>G | intron_variant | 1 | A1 | ||||
ENST00000508189.1 | n.1405G>C | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0395 AC: 5998AN: 151758Hom.: 312 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
5998
AN:
151758
Hom.:
Cov.:
33
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: 0.0568 AC: 118AN: 2078Hom.: 6 Cov.: 0 AF XY: 0.0578 AC XY: 63AN XY: 1090
GnomAD4 exome
AF:
AC:
118
AN:
2078
Hom.:
Cov.:
0
AF XY:
AC XY:
63
AN XY:
1090
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0397 AC: 6026AN: 151876Hom.: 320 Cov.: 33 AF XY: 0.0444 AC XY: 3293AN XY: 74238
GnomAD4 genome
?
AF:
AC:
6026
AN:
151876
Hom.:
Cov.:
33
AF XY:
AC XY:
3293
AN XY:
74238
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:
663
AN:
3446
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