rs10517756
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020116.5(FSTL5):c.161-6115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 151,738 control chromosomes in the GnomAD database, including 264 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 0.053 ( 264 hom., cov: 33)
Consequence
FSTL5
NM_020116.5 intron
NM_020116.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.26
Genes affected
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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 (NFE) allele frequency at 95% confidence interval = 0.0758 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FSTL5 | NM_020116.5 | c.161-6115G>A | intron_variant | ENST00000306100.10 | |||
FSTL5 | NM_001128427.3 | c.158-6115G>A | intron_variant | ||||
FSTL5 | NM_001128428.3 | c.158-6115G>A | intron_variant | ||||
FSTL5 | XM_011532126.1 | c.161-6115G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FSTL5 | ENST00000306100.10 | c.161-6115G>A | intron_variant | 1 | NM_020116.5 | P5 | |||
FSTL5 | ENST00000379164.8 | c.158-6115G>A | intron_variant | 1 | A1 | ||||
FSTL5 | ENST00000427802.2 | c.158-6115G>A | intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0527 AC: 7988AN: 151618Hom.: 264 Cov.: 33
GnomAD3 genomes
?
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151618
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0526 AC: 7983AN: 151738Hom.: 264 Cov.: 33 AF XY: 0.0505 AC XY: 3741AN XY: 74132
GnomAD4 genome
?
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AC:
7983
AN:
151738
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33
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3741
AN XY:
74132
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39
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3474
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at