rs9370986
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006366.3(CAP2):c.121+695T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 26)
Failed GnomAD Quality Control
Consequence
CAP2
NM_006366.3 intron
NM_006366.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.908
Genes affected
CAP2 (HGNC:20039): (cyclase associated actin cytoskeleton regulatory protein 2) This gene was identified by its similarity to the gene for human adenylyl cyclase-associated protein. The function of the protein encoded by this gene is unknown. However, the protein appears to be able to interact with adenylyl cyclase-associated protein and actin. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAP2 | NM_006366.3 | c.121+695T>A | intron_variant | ENST00000229922.7 | |||
CAP2 | NM_001363533.2 | c.121+695T>A | intron_variant | ||||
CAP2 | NM_001363534.2 | c.121+695T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAP2 | ENST00000229922.7 | c.121+695T>A | intron_variant | 1 | NM_006366.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 144418Hom.: 0 Cov.: 26 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 144418Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 70434
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70434
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ClinVar
Not reported inComputational scores
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Name
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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