rs563361414

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_021098.3(CACNA1H):c.5445+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000557 in 1,596,614 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00029 ( 0 hom., cov: 34)

Exomes 𝑓: 0.00059 ( 8 hom. )

Consequence

CACNA1H
NM_021098.3 splice_region, intron

Scores

Splicing: ADA: 0.00004677

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.130

Publications

0 publications found

Variant links:

Genes affected

CACNA1H (HGNC:1395): (calcium voltage-gated channel subunit alpha1 H) This gene encodes a T-type member of the alpha-1 subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. The alpha-1 subunit has 24 transmembrane segments and forms the pore through which ions pass into the cell. There are multiple isoforms of each of the proteins in the complex, either encoded by different genes or the result of alternative splicing of transcripts. Alternate transcriptional splice variants, encoding different isoforms, have been characterized for the gene described here. Studies suggest certain mutations in this gene lead to childhood absence epilepsy (CAE). [provided by RefSeq, Jul 2008]

CACNA1H Gene-Disease associations (from GenCC):

hyperaldosteronism, familial, type IV
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
childhood absence epilepsy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
epilepsy, childhood absence, susceptibility to, 6
Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

CACNA1H links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 16-1218047-G-A is Benign according to our data. Variant chr16-1218047-G-A is described in ClinVar as Benign. ClinVar VariationId is 529693.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000289 (44/152348) while in subpopulation SAS AF = 0.00891 (43/4824). AF 95% confidence interval is 0.0068. There are 0 homozygotes in GnomAd4. There are 29 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.

BS2

High AC in GnomAd4 at 44 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3 link	c.5445+7G>A		splice_region_variant, intron_variant	Intron 32 of 34	ENST00000348261.11	NP_066921.2	O95180-1B3KQH9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CACNA1H	ENST00000348261.11 link	c.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 34	1	NM_021098.3	ENSP00000334198.7	O95180-1
CACNA1H	ENST00000569107.6 link	c.5460+7G>A	splice_region_variant, intron_variant	Intron 31 of 33	1		ENSP00000454990.2	H3BNT0
CACNA1H	ENST00000711493.1 link	c.5463+7G>A	splice_region_variant, intron_variant	Intron 31 of 33			ENSP00000518778.1
CACNA1H	ENST00000565831.7 link	c.5427+7G>A	splice_region_variant, intron_variant	Intron 31 of 33	1		ENSP00000455840.1	O95180-2
CACNA1H	ENST00000711450.1 link	c.5460+7G>A	splice_region_variant, intron_variant	Intron 32 of 34			ENSP00000518762.1
CACNA1H	ENST00000564231.6 link	c.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 34	1		ENSP00000457555.2	H3BUA8
CACNA1H	ENST00000638323.1 link	c.5406+7G>A	splice_region_variant, intron_variant	Intron 32 of 34	5		ENSP00000492267.1	A0A1W2PR14
CACNA1H	ENST00000562079.6 link	c.5427+7G>A	splice_region_variant, intron_variant	Intron 31 of 33	1		ENSP00000454581.2	H3BMW6
CACNA1H	ENST00000711438.1 link	c.5388+7G>A	splice_region_variant, intron_variant	Intron 31 of 33			ENSP00000518754.1
CACNA1H	ENST00000711482.1 link	c.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 35			ENSP00000518771.1
CACNA1H	ENST00000711485.1 link	c.5427+7G>A	splice_region_variant, intron_variant	Intron 31 of 34			ENSP00000518774.1
CACNA1H	ENST00000711455.1 link	c.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 35			ENSP00000518768.1
CACNA1H	ENST00000711483.1 link	c.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 34			ENSP00000518772.1
CACNA1H	ENST00000711456.1 link	c.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 33			ENSP00000518769.1
CACNA1H	ENST00000621827.2 link	n.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 36	6		ENSP00000518766.1
CACNA1H	ENST00000637236.3 link	n.*1397+7G>A	splice_region_variant, intron_variant	Intron 31 of 33	5		ENSP00000492650.2	A0A1W2PS38
CACNA1H	ENST00000639478.1 link	n.*526+7G>A	splice_region_variant, intron_variant	Intron 32 of 34	5		ENSP00000491945.1	A0A1W2PQW2
CACNA1H	ENST00000640028.1 link	n.*3296+7G>A	splice_region_variant, intron_variant	Intron 32 of 34	5		ENSP00000491488.1	A0A1W2PQ19
CACNA1H	ENST00000711442.1 link	n.*4889+7G>A	splice_region_variant, intron_variant	Intron 30 of 33			ENSP00000518758.1
CACNA1H	ENST00000711448.1 link	n.*419+7G>A	splice_region_variant, intron_variant	Intron 33 of 35			ENSP00000518760.1
CACNA1H	ENST00000711449.1 link	n.*304+7G>A	splice_region_variant, intron_variant	Intron 32 of 34			ENSP00000518761.1
CACNA1H	ENST00000711451.1 link	n.*1057+7G>A	splice_region_variant, intron_variant	Intron 33 of 35			ENSP00000518763.1
CACNA1H	ENST00000711452.1 link	n.*112+7G>A	splice_region_variant, intron_variant	Intron 33 of 35			ENSP00000518764.1
CACNA1H	ENST00000711453.1 link	n.*112+7G>A	splice_region_variant, intron_variant	Intron 33 of 35			ENSP00000518765.1
CACNA1H	ENST00000711484.1 link	n.5427+7G>A	splice_region_variant, intron_variant	Intron 31 of 34			ENSP00000518773.1
CACNA1H	ENST00000711486.1 link	n.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 36			ENSP00000518775.1
CACNA1H	ENST00000711487.1 link	n.5445+7G>A	splice_region_variant, intron_variant	Intron 32 of 35			ENSP00000518776.1
CACNA1H	ENST00000711488.1 link	n.*561+7G>A	splice_region_variant, intron_variant	Intron 32 of 34			ENSP00000518777.1

Frequencies

GnomAD3 genomes

AF:

0.000289

AC:

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00891

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00127

AC:

285

AN:

224150

AF XY:

0.00169

show subpopulations

Gnomad AFR exome

AF:

0.0000784

Gnomad AMR exome

AF:

0.0000309

Gnomad ASJ exome

AF:

0.000106

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00126

GnomAD4 exome

AF:

0.000586

AC:

846

AN:

1444266

Hom.:

Cov.:

AF XY:

0.000853

AC XY:

611

AN XY:

716366

show subpopulations

African (AFR)

AF:

0.0000905

AC:

AN:

33162

American (AMR)

AF:

0.0000233

AC:

AN:

42984

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25772

East Asian (EAS)

AF:

0.00

AC:

AN:

38914

South Asian (SAS)

AF:

0.00940

AC:

787

AN:

83708

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50948

Middle Eastern (MID)

AF:

0.000349

AC:

AN:

5736

European-Non Finnish (NFE)

AF:

0.0000118

AC:

AN:

1103424

Other (OTH)

AF:

0.000671

AC:

AN:

59618

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

136

182

227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000289

AC:

AN:

152348

Hom.:

Cov.:

AF XY:

0.000389

AC XY:

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41586

American (AMR)

AF:

0.00

AC:

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00891

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68020

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000171

Hom.:

Bravo

AF:

0.0000378

Asia WGS

AF:

0.00260

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

CACNA1H-related disorder

Benign:1

Mar 25, 2019

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV

Benign:1

Aug 11, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.6

(source)

DANN

Benign

0.78

PhyloP100

-0.13

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000047

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over