X-49212906-T-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001256789.3(CACNA1F):c.3813+68A>G 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 0.64 ( 16365 hom., 19853 hem., cov: 21)
Exomes 𝑓: 0.68 ( 167935 hom. 231952 hem. )
Failed GnomAD Quality Control
Consequence
CACNA1F
NM_001256789.3 intron
NM_001256789.3 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.673
Genes affected
CACNA1F (HGNC:1393): (calcium voltage-gated channel subunit alpha1 F) This gene encodes a multipass transmembrane protein that functions as an alpha-1 subunit of the voltage-dependent calcium channel, which mediates the influx of calcium ions into the cell. The encoded protein forms a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. Mutations in this gene can cause X-linked eye disorders, including congenital stationary night blindness type 2A, cone-rod dystropy, and Aland Island eye disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2013]
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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=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.3813+68A>G | intron_variant | ENST00000323022.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.3813+68A>G | intron_variant | 1 | NM_001256789.3 | ||||
CACNA1F | ENST00000376251.5 | c.3651+68A>G | intron_variant | 1 | |||||
CACNA1F | ENST00000376265.2 | c.3846+68A>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.636 AC: 69597AN: 109435Hom.: 16373 Cov.: 21 AF XY: 0.624 AC XY: 19804AN XY: 31747
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.680 AC: 722129AN: 1061603Hom.: 167935 Cov.: 25 AF XY: 0.694 AC XY: 231952AN XY: 334185
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.636 AC: 69622AN: 109490Hom.: 16365 Cov.: 21 AF XY: 0.624 AC XY: 19853AN XY: 31812
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at