rs10520514
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The XM_017008385.2(TENM3):c.-236-6360T>A variant causes a intron change. The variant allele was found at a frequency of 0.309 in 152,020 control chromosomes in the GnomAD database, including 8,100 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 0.31 ( 8100 hom., cov: 32)
Consequence
TENM3
XM_017008385.2 intron
XM_017008385.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.26
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM3 | XM_017008385.2 | c.-236-6360T>A | intron_variant | ||||
TENM3 | XM_017008389.2 | c.-236-6360T>A | intron_variant | ||||
TENM3 | XM_017008390.2 | c.-236-6360T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes ? AF: 0.309 AC: 46945AN: 151902Hom.: 8097 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.309 AC: 46963AN: 152020Hom.: 8100 Cov.: 32 AF XY: 0.308 AC XY: 22851AN XY: 74312
GnomAD4 genome
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46963
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152020
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32
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22851
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74312
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Asia WGS
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944
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at