16-1153753-C-T

Variant names:

• chr16-1153753-C-T
• rs1257574455
• NM_021098.3:c.16C>T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_021098.3(CACNA1H):​c.16C>T​(p.Arg6Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000942 in 1,061,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 30)
  • Exomes 𝑓: 9.4e-7 (0 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.27733707).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.16C>T	p.Arg6Trp	missense_variant	Exon 2 of 35	ENST00000348261.11	NP_066921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1H	ENST00000348261.11	c.16C>T	p.Arg6Trp	missense_variant	Exon 2 of 35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000565831.6	c.16C>T	p.Arg6Trp	missense_variant	Exon 1 of 33	1		ENSP00000455840.1
CACNA1H	ENST00000638323.1	c.16C>T	p.Arg6Trp	missense_variant	Exon 2 of 35	5		ENSP00000492267.1
CACNA1H	ENST00000639478.1	n.16C>T		non_coding_transcript_exon_variant	Exon 2 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.16C>T		non_coding_transcript_exon_variant	Exon 2 of 35	5		ENSP00000491488.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 9.42e-7 AC: 1 AN: 1061726 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 502314

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000135

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.027	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.13	T;.;.;.
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.34
FATHMM_MKL	Benign	0.56	D
LIST_S2	Benign	0.72	T;T;T;.
M_CAP	Pathogenic	0.85	D
MetaRNN	Benign	0.28	T;T;T;T
MetaSVM	Uncertain	0.19	D
MutationAssessor	Benign	0.0	N;.;N;N
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.78	N;.;N;N
REVEL	Uncertain	0.30
Sift	Uncertain	0.024	D;.;D;D
Sift4G	Uncertain	0.055	T;.;T;T
Polyphen		0.77	P;.;P;P
Vest4		0.12
MutPred		0.28		Loss of MoRF binding (P = 0.0255);Loss of MoRF binding (P = 0.0255);Loss of MoRF binding (P = 0.0255);Loss of MoRF binding (P = 0.0255);
MVP		0.32
ClinPred		0.30	T
GERP RS		2.9
Varity_R		0.14
gMVP		0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1257574455; hg19: chr16-1203753;