rs16901979
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000642100(CASC19):n.418-33538G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152026 control chromosomes in the gnomAD Genomes database, including 4275 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 0.16 ( 4275 hom., cov: 32)
Consequence
CASC19
ENST00000642100 intron, non_coding_transcript
ENST00000642100 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.805
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASC19 | ENST00000642100.1 | n.418-33538G>T | intron_variant, non_coding_transcript_variant | ||||||
PCAT1 | ENST00000645463.1 | n.855+106053C>A | intron_variant, non_coding_transcript_variant | ||||||
PCAT1 | ENST00000646670.1 | n.1064+98897C>A | intron_variant, non_coding_transcript_variant | ||||||
PCAT1 | ENST00000647190.2 | n.1191+63371C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.157 AC: 23857AN: 152026Hom.: 4275 Cov.: 32
GnomAD3 genomes
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23857
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152026
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Cov.:
32
Gnomad AFR
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Asia WGS
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AC:
508
AN:
3476
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