rs774915687

Positions:

• chr16-1220273-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Moderate BP6_Moderate BS2

The NM_021098.3(CACNA1H):​c.6341C>T​(p.Thr2114Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000488 in 1,434,024 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 35)
  • Exomes 𝑓: 0.0000049 (1 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.385

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.15644568).
• BP6: Variant 16-1220273-C-T is Benign according to our data. Variant chr16-1220273-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 529615.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAdExome4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.6341C>T	p.Thr2114Ile	missense_variant	35/35	ENST00000348261.11	NP_066921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1H	ENST00000348261.11	c.6341C>T	p.Thr2114Ile	missense_variant	35/35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000565831.6	c.6323C>T	p.Thr2108Ile	missense_variant	33/33	1		ENSP00000455840.1
CACNA1H	ENST00000638323.1	c.6302C>T	p.Thr2101Ile	missense_variant	35/35	5		ENSP00000492267.1
CACNA1H	ENST00000569107.5	c.2579C>T	p.Thr860Ile	missense_variant	17/17	1		ENSP00000454990.2
CACNA1H	ENST00000564231.5	c.2531C>T	p.Thr844Ile	missense_variant	18/18	1		ENSP00000457555.2
CACNA1H	ENST00000562079.5	c.2513C>T	p.Thr838Ile	missense_variant	17/17	1		ENSP00000454581.2
CACNA1H	ENST00000639478.1	n.*1389C>T		non_coding_transcript_exon_variant	35/35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.*4159C>T		non_coding_transcript_exon_variant	35/35	5		ENSP00000491488.1
CACNA1H	ENST00000639478.1	n.*1389C>T		3_prime_UTR_variant	35/35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.*4159C>T		3_prime_UTR_variant	35/35	5		ENSP00000491488.1

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD3 exomes AF: 0.0000142 AC: 3 AN: 211610 Hom.: 1 AF XY: 0.0000252 AC XY: 3 AN XY: 119050

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000697

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000189

GnomAD4 exome AF: 0.00000488 AC: 7 AN: 1434024 Hom.: 1 Cov.: 73 AF XY: 0.00000701 AC XY: 5 AN XY: 713164

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000236

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000272

Gnomad4 OTH exome AF: 0.0000336

GnomAD4 genome Cov.: 35

ExAC AF: 0.0000172 AC: 2

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 02, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	0.0029	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	8.3
DANN	Benign	0.79
DEOGEN2	Benign	0.13	T;.;.;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.15	N
LIST_S2	Benign	0.41	T;T;T;.
M_CAP	Pathogenic	0.86	D
MetaRNN	Benign	0.16	T;T;T;T
MetaSVM	Uncertain	-0.045	T
MutationAssessor	Benign	0.34	N;.;.;.
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	-0.89	N;.;N;N
REVEL	Uncertain	0.31
Sift	Benign	0.28	T;.;T;T
Sift4G	Benign	0.17	T;.;T;T
Polyphen		0.0020	B;.;B;B
Vest4		0.055
MVP		0.49
ClinPred		0.023	T
GERP RS		-0.32
Varity_R		0.050
gMVP		0.10

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

LitVar

Other links and lift over

dbSNP: rs774915687; hg19: chr16-1270273;