rs186422070

Variant names:

• chr16-1219006-C-G
• rs186422070
• NM_021098.3:c.5924C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-1219006-C-G
• chr16-1219006-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_021098.3(CACNA1H):​c.5924C>G​(p.Ser1975Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict 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: 31)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20802376).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.5924C>G	p.Ser1975Cys	missense_variant	Exon 34 of 35	ENST00000348261.11	NP_066921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1H	ENST00000348261.11	c.5924C>G	p.Ser1975Cys	missense_variant	Exon 34 of 35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000565831.6	c.5906C>G	p.Ser1969Cys	missense_variant	Exon 32 of 33	1		ENSP00000455840.1
CACNA1H	ENST00000638323.1	c.5885C>G	p.Ser1962Cys	missense_variant	Exon 34 of 35	5		ENSP00000492267.1
CACNA1H	ENST00000569107.5	c.2162C>G	p.Ser721Cys	missense_variant	Exon 16 of 17	1		ENSP00000454990.2
CACNA1H	ENST00000564231.5	c.2114C>G	p.Ser705Cys	missense_variant	Exon 17 of 18	1		ENSP00000457555.2
CACNA1H	ENST00000562079.5	c.2096C>G	p.Ser699Cys	missense_variant	Exon 16 of 17	1		ENSP00000454581.2
CACNA1H	ENST00000639478.1	n.*972C>G		non_coding_transcript_exon_variant	Exon 34 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.*3742C>G		non_coding_transcript_exon_variant	Exon 34 of 35	5		ENSP00000491488.1
CACNA1H	ENST00000639478.1	n.*972C>G		3_prime_UTR_variant	Exon 34 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.*3742C>G		3_prime_UTR_variant	Exon 34 of 35	5		ENSP00000491488.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD3 exomes AF: 0.00000647 AC: 1 AN: 154606 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 82232

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: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000168

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.15e-7 AC: 1 AN: 1398026 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 689542

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.27e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Uncertain	-0.030
CADD	Benign	20
DANN	Benign	0.97
DEOGEN2	Benign	0.26	T;.;.;.
Eigen	Benign	-0.20
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.21	N
LIST_S2	Benign	0.69	T;T;T;.
M_CAP	Pathogenic	0.40	D
MetaRNN	Benign	0.21	T;T;T;T
MetaSVM	Uncertain	0.37	D
MutationAssessor	Benign	1.8	L;.;.;.
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-2.2	N;.;N;N
REVEL	Uncertain	0.32
Sift	Uncertain	0.020	D;.;D;D
Sift4G	Uncertain	0.035	D;.;D;D
Polyphen		0.89	P;.;D;D
Vest4		0.18
MutPred		0.16		Loss of phosphorylation at S1975 (P = 0.0449);.;.;.;
MVP		0.85
ClinPred		0.22	T
GERP RS		3.5
Varity_R		0.19
gMVP		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs186422070; hg19: chr16-1269006;