rs2071316

chrX-49212906-T-CchrX-49212906-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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
• 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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS2: High Homozygotes in GnomAd at 16373 XL gene

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: 69597 AN: 109435 Hom.: 16373 Cov.: 21 AF XY: 0.624 AC XY: 19804 AN XY: 31747

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.716

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.639

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.680 AC: 722129 AN: 1061603 Hom.: 167935 Cov.: 25 AF XY: 0.694 AC XY: 231952 AN XY: 334185

Gnomad4 AFR exome AF: 0.590

Gnomad4 AMR exome AF: 0.399

Gnomad4 ASJ exome AF: 0.777

Gnomad4 EAS exome AF: 0.347

Gnomad4 SAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.637

Gnomad4 NFE exome AF: 0.706

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.636 AC: 69622 AN: 109490 Hom.: 16365 Cov.: 21 AF XY: 0.624 AC XY: 19853 AN XY: 31812

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.641

Alfa AF: 0.690 Hom.: 69534

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2071316; hg19: chrX-49069366;