rs9893818
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The XM_017023997.2(C17orf99):c.112C>A(p.Arg38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0349 in 152,246 control chromosomes in the GnomAD database, including 317 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 0.035 ( 317 hom., cov: 30)
Consequence
C17orf99
XM_017023997.2 synonymous
XM_017023997.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.417
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP7
?
Synonymous conserved (PhyloP=-0.417 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C17orf99 | XM_017023997.2 | c.112C>A | p.Arg38= | synonymous_variant | 1/4 | ||
C17orf99 | XM_011524152.3 | c.112C>A | p.Arg38= | synonymous_variant | 1/5 | ||
C17orf99 | XM_047435058.1 | c.112C>A | p.Arg38= | synonymous_variant | 1/6 | ||
C17orf99 | XM_047435061.1 | c.112C>A | p.Arg38= | synonymous_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0349 AC: 5307AN: 152128Hom.: 317 Cov.: 30
GnomAD3 genomes
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0349 AC: 5314AN: 152246Hom.: 317 Cov.: 30 AF XY: 0.0332 AC XY: 2468AN XY: 74432
GnomAD4 genome
?
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AC:
5314
AN:
152246
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30
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2468
AN XY:
74432
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at