rs11796927
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001256789.3(CACNA1F):c.26-182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 110,152 control chromosomes in the GnomAD database, including 175 homozygotes. There are 1,576 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.051 ( 175 hom., 1576 hem., cov: 22)
Consequence
CACNA1F
NM_001256789.3 intron
NM_001256789.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.91
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant X-49232109-T-C is Benign according to our data. Variant chrX-49232109-T-C is described in ClinVar as [Benign]. Clinvar id is 1272957.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0766 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.26-182A>G | intron_variant | ENST00000323022.10 | |||
CACNA1F | NM_001256790.3 | c.66-417A>G | intron_variant | ||||
CACNA1F | NM_005183.4 | c.26-182A>G | intron_variant | ||||
CACNA1F | XM_011543983.3 | c.66-417A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.26-182A>G | intron_variant | 1 | NM_001256789.3 | ||||
CACNA1F | ENST00000376251.5 | c.66-417A>G | intron_variant | 1 | |||||
CACNA1F | ENST00000376265.2 | c.26-182A>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0508 AC: 5589AN: 110109Hom.: 176 Cov.: 22 AF XY: 0.0484 AC XY: 1576AN XY: 32537
GnomAD3 genomes
?
AF:
AC:
5589
AN:
110109
Hom.:
Cov.:
22
AF XY:
AC XY:
1576
AN XY:
32537
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0507 AC: 5585AN: 110152Hom.: 175 Cov.: 22 AF XY: 0.0484 AC XY: 1576AN XY: 32592
GnomAD4 genome
?
AF:
AC:
5585
AN:
110152
Hom.:
Cov.:
22
AF XY:
AC XY:
1576
AN XY:
32592
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at