chrX-49231025-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001256789.3(CACNA1F):​c.382-36T>C 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 ( 16505 hom., 15315 hem., cov: 18)
Exomes 𝑓: 0.68 ( 154208 hom. 189773 hem. )
Failed GnomAD Quality Control

Consequence

CACNA1F
NM_001256789.3 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.163
Variant links:
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 Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1FNM_001256789.3 linkuse as main transcriptc.382-36T>C intron_variant ENST00000323022.10 NP_001243718.1
CACNA1FNM_001256790.3 linkuse as main transcriptc.187-36T>C intron_variant NP_001243719.1
CACNA1FNM_005183.4 linkuse as main transcriptc.382-36T>C intron_variant NP_005174.2
CACNA1FXM_011543983.3 linkuse as main transcriptc.187-36T>C intron_variant XP_011542285.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNA1FENST00000323022.10 linkuse as main transcriptc.382-36T>C intron_variant 1 NM_001256789.3 ENSP00000321618 O60840-2
CACNA1FENST00000376251.5 linkuse as main transcriptc.187-36T>C intron_variant 1 ENSP00000365427 O60840-4
CACNA1FENST00000376265.2 linkuse as main transcriptc.382-36T>C intron_variant 1 ENSP00000365441 P1O60840-1

Frequencies

GnomAD3 genomes
AF:
0.638
AC:
65030
AN:
101992
Hom.:
16512
Cov.:
18
AF XY:
0.603
AC XY:
15271
AN XY:
25318
show subpopulations
Gnomad AFR
AF:
0.557
Gnomad AMI
AF:
0.623
Gnomad AMR
AF:
0.532
Gnomad ASJ
AF:
0.788
Gnomad EAS
AF:
0.328
Gnomad SAS
AF:
0.658
Gnomad FIN
AF:
0.620
Gnomad MID
AF:
0.750
Gnomad NFE
AF:
0.714
Gnomad OTH
AF:
0.641
GnomAD4 exome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.681
AC:
630167
AN:
925689
Hom.:
154208
Cov.:
16
AF XY:
0.678
AC XY:
189773
AN XY:
279755
show subpopulations
Gnomad4 AFR exome
AF:
0.544
Gnomad4 AMR exome
AF:
0.483
Gnomad4 ASJ exome
AF:
0.775
Gnomad4 EAS exome
AF:
0.344
Gnomad4 SAS exome
AF:
0.697
Gnomad4 FIN exome
AF:
0.653
Gnomad4 NFE exome
AF:
0.708
Gnomad4 OTH exome
AF:
0.668
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.638
AC:
65055
AN:
102037
Hom.:
16505
Cov.:
18
AF XY:
0.604
AC XY:
15315
AN XY:
25375
show subpopulations
Gnomad4 AFR
AF:
0.557
Gnomad4 AMR
AF:
0.532
Gnomad4 ASJ
AF:
0.788
Gnomad4 EAS
AF:
0.328
Gnomad4 SAS
AF:
0.662
Gnomad4 FIN
AF:
0.620
Gnomad4 NFE
AF:
0.714
Gnomad4 OTH
AF:
0.644
Alfa
AF:
0.593
Hom.:
5504
Bravo
AF:
0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5905724; hg19: chrX-49087487; API