rs5905724

Variant names:

• chrX-49231025-A-C
• rs5905724
• NM_001256789.3:c.382-36T>G

Your query was ambiguous. Multiple possible variants found:

• chrX-49231025-A-C
• chrX-49231025-A-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001256789.3(CACNA1F):​c.382-36T>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: not found (cov: 18)
  • Exomes 𝑓: 0.0000011 (0 hom. 0 hem.)
• Consequence: CACNA1F NM_001256789.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 0 publications found

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]

CACNA1F Gene-Disease associations (from GenCC):

• Aland island eye disease

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
• inherited retinal dystrophy

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• congenital stationary night blindness 2A

  Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• X-linked cone-rod dystrophy 3

  Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• cone-rod dystrophy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• congenital stationary night blindness

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1F	NM_001256789.3	c.382-36T>G		intron_variant	Intron 3 of 47	ENST00000323022.10	NP_001243718.1
CACNA1F	NM_005183.4	c.382-36T>G		intron_variant	Intron 3 of 47		NP_005174.2
CACNA1F	NM_001256790.3	c.187-36T>G		intron_variant	Intron 3 of 47		NP_001243719.1
CACNA1F	XM_011543983.3	c.187-36T>G		intron_variant	Intron 3 of 46		XP_011542285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1F	ENST00000323022.10	c.382-36T>G		intron_variant	Intron 3 of 47	1	NM_001256789.3	ENSP00000321618.6
CACNA1F	ENST00000376265.2	c.382-36T>G		intron_variant	Intron 3 of 47	1		ENSP00000365441.2
CACNA1F	ENST00000376251.5	c.187-36T>G		intron_variant	Intron 3 of 47	1		ENSP00000365427.1

Frequencies

GnomAD3 genomes Cov.: 18

GnomAD4 exome AF: 0.00000108 AC: 1 AN: 928360 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 279942

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 23331

American (AMR) AF: 0.00 AC: 0 AN: 33619

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18085

East Asian (EAS) AF: 0.00 AC: 0 AN: 29080

South Asian (SAS) AF: 0.00 AC: 0 AN: 49322

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39263

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3757

European-Non Finnish (NFE) AF: 0.00000145 AC: 1 AN: 691495

Other (OTH) AF: 0.00 AC: 0 AN: 40408

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 18

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
PhyloP100		-0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs5905724; hg19: chrX-49087487;