rs284320
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001079843.3(CASZ1):c.17-1392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,128 control chromosomes in the GnomAD database, including 7,045 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 0.28 ( 7045 hom., cov: 33)
Consequence
CASZ1
NM_001079843.3 intron
NM_001079843.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.509
Genes affected
CASZ1 (HGNC:26002): (castor zinc finger 1) The protein encoded by this gene is a zinc finger transcription factor. The encoded protein may function as a tumor suppressor, and single nucleotide polymorphisms in this gene are associated with blood pressure variation. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASZ1 | NM_001079843.3 | c.17-1392A>G | intron_variant | ENST00000377022.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASZ1 | ENST00000377022.8 | c.17-1392A>G | intron_variant | 1 | NM_001079843.3 | P1 | |||
CASZ1 | ENST00000344008.5 | c.17-1392A>G | intron_variant | 2 | |||||
CASZ1 | ENST00000478728.2 | n.40-1392A>G | intron_variant, non_coding_transcript_variant | 5 | |||||
CASZ1 | ENST00000496432.6 | n.223-1392A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 43000AN: 152008Hom.: 7010 Cov.: 33
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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: 0.283 AC: 43083AN: 152128Hom.: 7045 Cov.: 33 AF XY: 0.287 AC XY: 21327AN XY: 74372
GnomAD4 genome
?
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33
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21327
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74372
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895
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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