NM_021098.3:c.5382C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_021098.3(CACNA1H):c.5382C>T(p.Phe1794Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,605,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 34)

Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

CACNA1H
NM_021098.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.79

Publications

1 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 -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 16-1217977-C-T is Benign according to our data. Variant chr16-1217977-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 460142.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.79 with no splicing effect.

BS2

High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 35	ENST00000348261.11	NP_066921.2	O95180-1B3KQH9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CACNA1H	ENST00000348261.11 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 35	1	NM_021098.3	ENSP00000334198.7	O95180-1
CACNA1H	ENST00000569107.6 link	c.5397C>T	p.Phe1799Phe	synonymous_variant	Exon 31 of 34	1		ENSP00000454990.2	H3BNT0
CACNA1H	ENST00000711493.1 link	c.5400C>T	p.Phe1800Phe	synonymous_variant	Exon 31 of 34			ENSP00000518778.1
CACNA1H	ENST00000565831.7 link	c.5364C>T	p.Phe1788Phe	synonymous_variant	Exon 31 of 34	1		ENSP00000455840.1	O95180-2
CACNA1H	ENST00000711450.1 link	c.5397C>T	p.Phe1799Phe	synonymous_variant	Exon 32 of 35			ENSP00000518762.1
CACNA1H	ENST00000564231.6 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 35	1		ENSP00000457555.2	H3BUA8
CACNA1H	ENST00000638323.1 link	c.5343C>T	p.Phe1781Phe	synonymous_variant	Exon 32 of 35	5		ENSP00000492267.1	A0A1W2PR14
CACNA1H	ENST00000562079.6 link	c.5364C>T	p.Phe1788Phe	synonymous_variant	Exon 31 of 34	1		ENSP00000454581.2	H3BMW6
CACNA1H	ENST00000711438.1 link	c.5325C>T	p.Phe1775Phe	synonymous_variant	Exon 31 of 34			ENSP00000518754.1
CACNA1H	ENST00000711482.1 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 36			ENSP00000518771.1
CACNA1H	ENST00000711485.1 link	c.5364C>T	p.Phe1788Phe	synonymous_variant	Exon 31 of 35			ENSP00000518774.1
CACNA1H	ENST00000711455.1 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 36			ENSP00000518768.1
CACNA1H	ENST00000711483.1 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 35			ENSP00000518772.1
CACNA1H	ENST00000711456.1 link	c.5382C>T	p.Phe1794Phe	synonymous_variant	Exon 32 of 34			ENSP00000518769.1
CACNA1H	ENST00000621827.2 link	n.5382C>T		non_coding_transcript_exon_variant	Exon 32 of 37	6		ENSP00000518766.1
CACNA1H	ENST00000637236.3 link	n.*1334C>T		non_coding_transcript_exon_variant	Exon 31 of 34	5		ENSP00000492650.2	A0A1W2PS38
CACNA1H	ENST00000639478.1 link	n.*463C>T		non_coding_transcript_exon_variant	Exon 32 of 35	5		ENSP00000491945.1	A0A1W2PQW2
CACNA1H	ENST00000640028.1 link	n.*3233C>T		non_coding_transcript_exon_variant	Exon 32 of 35	5		ENSP00000491488.1	A0A1W2PQ19
CACNA1H	ENST00000711442.1 link	n.*4826C>T		non_coding_transcript_exon_variant	Exon 30 of 34			ENSP00000518758.1
CACNA1H	ENST00000711448.1 link	n.*356C>T		non_coding_transcript_exon_variant	Exon 33 of 36			ENSP00000518760.1
CACNA1H	ENST00000711449.1 link	n.*241C>T		non_coding_transcript_exon_variant	Exon 32 of 35			ENSP00000518761.1
CACNA1H	ENST00000711451.1 link	n.*994C>T		non_coding_transcript_exon_variant	Exon 33 of 36			ENSP00000518763.1
CACNA1H	ENST00000711452.1 link	n.*49C>T		non_coding_transcript_exon_variant	Exon 33 of 36			ENSP00000518764.1
CACNA1H	ENST00000711453.1 link	n.*49C>T		non_coding_transcript_exon_variant	Exon 33 of 36			ENSP00000518765.1
CACNA1H	ENST00000711484.1 link	n.5364C>T		non_coding_transcript_exon_variant	Exon 31 of 35			ENSP00000518773.1
CACNA1H	ENST00000711486.1 link	n.5382C>T		non_coding_transcript_exon_variant	Exon 32 of 37			ENSP00000518775.1
CACNA1H	ENST00000711487.1 link	n.5382C>T		non_coding_transcript_exon_variant	Exon 32 of 36			ENSP00000518776.1
CACNA1H	ENST00000711488.1 link	n.*498C>T		non_coding_transcript_exon_variant	Exon 32 of 35			ENSP00000518777.1
CACNA1H	ENST00000637236.3 link	n.*1334C>T		3_prime_UTR_variant	Exon 31 of 34	5		ENSP00000492650.2	A0A1W2PS38
CACNA1H	ENST00000639478.1 link	n.*463C>T		3_prime_UTR_variant	Exon 32 of 35	5		ENSP00000491945.1	A0A1W2PQW2
CACNA1H	ENST00000640028.1 link	n.*3233C>T		3_prime_UTR_variant	Exon 32 of 35	5		ENSP00000491488.1	A0A1W2PQ19
CACNA1H	ENST00000711442.1 link	n.*4826C>T		3_prime_UTR_variant	Exon 30 of 34			ENSP00000518758.1
CACNA1H	ENST00000711448.1 link	n.*356C>T		3_prime_UTR_variant	Exon 33 of 36			ENSP00000518760.1
CACNA1H	ENST00000711449.1 link	n.*241C>T		3_prime_UTR_variant	Exon 32 of 35			ENSP00000518761.1
CACNA1H	ENST00000711451.1 link	n.*994C>T		3_prime_UTR_variant	Exon 33 of 36			ENSP00000518763.1
CACNA1H	ENST00000711452.1 link	n.*49C>T		3_prime_UTR_variant	Exon 33 of 36			ENSP00000518764.1
CACNA1H	ENST00000711453.1 link	n.*49C>T		3_prime_UTR_variant	Exon 33 of 36			ENSP00000518765.1
CACNA1H	ENST00000711488.1 link	n.*498C>T		3_prime_UTR_variant	Exon 32 of 35			ENSP00000518777.1

Frequencies

GnomAD3 genomes

AF:

0.0000525

AC:

AN:

152250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000386

AC:

AN:

233362

AF XY:

0.0000315

show subpopulations

Gnomad AFR exome

AF:

0.000145

Gnomad AMR exome

AF:

0.0000903

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000588

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000191

Gnomad OTH exome

AF:

0.000175

GnomAD4 exome

AF:

0.0000103

AC:

AN:

1452760

Hom.:

Cov.:

AF XY:

0.00000831

AC XY:

AN XY:

721860

show subpopulations

African (AFR)

AF:

0.000120

AC:

AN:

33300

American (AMR)

AF:

0.0000456

AC:

AN:

43904

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25916

East Asian (EAS)

AF:

0.00

AC:

AN:

39274

South Asian (SAS)

AF:

0.00

AC:

AN:

84602

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51446

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5760

European-Non Finnish (NFE)

AF:

0.00000541

AC:

AN:

1108514

Other (OTH)

AF:

0.0000500

AC:

AN:

60044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.0000525

AC:

AN:

152368

Hom.:

Cov.:

AF XY:

0.0000805

AC XY:

AN XY:

74514

show subpopulations

African (AFR)

AF:

0.000120

AC:

AN:

41590

American (AMR)

AF:

0.00

AC:

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5178

South Asian (SAS)

AF:

0.000207

AC:

AN:

4832

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:

68032

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.000102

Hom.:

Bravo

AF:

0.0000756

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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

Benign:1

Jan 22, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.32

CADD

Benign

6.9

(source)

DANN

Benign

0.94

PhyloP100

-1.8

Splicing

Name

Calibrated prediction

Score

Prediction

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

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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