X-49205164-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001256789.3(CACNA1F):c.5874C>T(p.Asp1958=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,207,982 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 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 0.000018 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000011 ( 0 hom. 3 hem. )
Consequence
CACNA1F
NM_001256789.3 synonymous
NM_001256789.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.17
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant X-49205164-G-A is Benign according to our data. Variant chrX-49205164-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1136539.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.17 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.5874C>T | p.Asp1958= | synonymous_variant | 48/48 | ENST00000323022.10 | NP_001243718.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.5874C>T | p.Asp1958= | synonymous_variant | 48/48 | 1 | NM_001256789.3 | ENSP00000321618 | ||
CACNA1F | ENST00000376265.2 | c.5907C>T | p.Asp1969= | synonymous_variant | 48/48 | 1 | ENSP00000365441 | P1 | ||
CACNA1F | ENST00000376251.5 | c.5712C>T | p.Asp1904= | synonymous_variant | 48/48 | 1 | ENSP00000365427 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112166Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34312
GnomAD3 genomes
AF:
AC:
2
AN:
112166
Hom.:
Cov.:
22
AF XY:
AC XY:
0
AN XY:
34312
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:
GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181656Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66442
GnomAD3 exomes
AF:
AC:
1
AN:
181656
Hom.:
AF XY:
AC XY:
1
AN XY:
66442
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000110 AC: 12AN: 1095816Hom.: 0 Cov.: 30 AF XY: 0.00000830 AC XY: 3AN XY: 361310
GnomAD4 exome
AF:
AC:
12
AN:
1095816
Hom.:
Cov.:
30
AF XY:
AC XY:
3
AN XY:
361310
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112166Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34312
GnomAD4 genome
AF:
AC:
2
AN:
112166
Hom.:
Cov.:
22
AF XY:
AC XY:
0
AN XY:
34312
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 04, 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