rs199764042
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001256789.3(CACNA1F):c.3439-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0026 in 1,207,806 control chromosomes in the GnomAD database, including 5 homozygotes. There are 1,084 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0019 ( 0 hom., 51 hem., cov: 22)
Exomes 𝑓: 0.0027 ( 5 hom. 1033 hem. )
Consequence
CACNA1F
NM_001256789.3 intron
NM_001256789.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.20
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 Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant X-49215262-G-A is Benign according to our data. Variant chrX-49215262-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 445846.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-49215262-G-A is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00189 (209/110691) while in subpopulation SAS AF= 0.0043 (11/2560). AF 95% confidence interval is 0.00241. There are 0 homozygotes in gnomad4. There are 51 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd4 at 51 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.3439-18C>T | intron_variant | ENST00000323022.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.3439-18C>T | intron_variant | 1 | NM_001256789.3 | ||||
CACNA1F | ENST00000376251.5 | c.3277-18C>T | intron_variant | 1 | |||||
CACNA1F | ENST00000376265.2 | c.3472-18C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00190 AC: 210AN: 110640Hom.: 0 Cov.: 22 AF XY: 0.00155 AC XY: 51AN XY: 32836
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GnomAD3 exomes AF: 0.00278 AC: 504AN: 181566Hom.: 5 AF XY: 0.00314 AC XY: 208AN XY: 66140
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GnomAD4 exome AF: 0.00268 AC: 2937AN: 1097115Hom.: 5 Cov.: 32 AF XY: 0.00285 AC XY: 1033AN XY: 362507
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GnomAD4 genome ? AF: 0.00189 AC: 209AN: 110691Hom.: 0 Cov.: 22 AF XY: 0.00155 AC XY: 51AN XY: 32897
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 15, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Ocular albinism, type II Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Congenital stationary night blindness 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
X-linked cone-rod dystrophy 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational 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