16-1220866-A-G
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_021098.3(CACNA1H):c.6934A>G(p.Met2312Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,612,560 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021098.3 missense
Scores
Clinical Significance
Conservation
Publications
- hyperaldosteronism, familial, type IVInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- childhood absence epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- epilepsy, childhood absence, susceptibility to, 6Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.6934A>G | p.Met2312Val | missense_variant | Exon 35 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000569107.6 | c.6949A>G | p.Met2317Val | missense_variant | Exon 34 of 34 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000711493.1 | c.6919A>G | p.Met2307Val | missense_variant | Exon 34 of 34 | ENSP00000518778.1 | ||||
CACNA1H | ENST00000565831.7 | c.6916A>G | p.Met2306Val | missense_variant | Exon 34 of 34 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000711450.1 | c.6916A>G | p.Met2306Val | missense_variant | Exon 35 of 35 | ENSP00000518762.1 | ||||
CACNA1H | ENST00000564231.6 | c.6901A>G | p.Met2301Val | missense_variant | Exon 35 of 35 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000638323.1 | c.6895A>G | p.Met2299Val | missense_variant | Exon 35 of 35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000562079.6 | c.6883A>G | p.Met2295Val | missense_variant | Exon 34 of 34 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000711438.1 | c.6877A>G | p.Met2293Val | missense_variant | Exon 34 of 34 | ENSP00000518754.1 | ||||
CACNA1H | ENST00000637236.3 | n.*2853A>G | non_coding_transcript_exon_variant | Exon 34 of 34 | 5 | ENSP00000492650.2 | ||||
CACNA1H | ENST00000639478.1 | n.*1982A>G | non_coding_transcript_exon_variant | Exon 35 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*4752A>G | non_coding_transcript_exon_variant | Exon 35 of 35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000711442.1 | n.*6378A>G | non_coding_transcript_exon_variant | Exon 33 of 34 | ENSP00000518758.1 | |||||
CACNA1H | ENST00000711448.1 | n.*1875A>G | non_coding_transcript_exon_variant | Exon 36 of 36 | ENSP00000518760.1 | |||||
CACNA1H | ENST00000711449.1 | n.*1793A>G | non_coding_transcript_exon_variant | Exon 35 of 35 | ENSP00000518761.1 | |||||
CACNA1H | ENST00000711451.1 | n.*2513A>G | non_coding_transcript_exon_variant | Exon 36 of 36 | ENSP00000518763.1 | |||||
CACNA1H | ENST00000711452.1 | n.*1601A>G | non_coding_transcript_exon_variant | Exon 36 of 36 | ENSP00000518764.1 | |||||
CACNA1H | ENST00000711453.1 | n.*1568A>G | non_coding_transcript_exon_variant | Exon 36 of 36 | ENSP00000518765.1 | |||||
CACNA1H | ENST00000711484.1 | n.*848A>G | non_coding_transcript_exon_variant | Exon 34 of 35 | ENSP00000518773.1 | |||||
CACNA1H | ENST00000711486.1 | n.6934A>G | non_coding_transcript_exon_variant | Exon 35 of 37 | ENSP00000518775.1 | |||||
CACNA1H | ENST00000711487.1 | n.6901A>G | non_coding_transcript_exon_variant | Exon 35 of 36 | ENSP00000518776.1 | |||||
CACNA1H | ENST00000711488.1 | n.*2050A>G | non_coding_transcript_exon_variant | Exon 35 of 35 | ENSP00000518777.1 | |||||
CACNA1H | ENST00000711482.1 | c.*413A>G | 3_prime_UTR_variant | Exon 36 of 36 | ENSP00000518771.1 | |||||
CACNA1H | ENST00000711485.1 | c.*413A>G | 3_prime_UTR_variant | Exon 35 of 35 | ENSP00000518774.1 | |||||
CACNA1H | ENST00000711455.1 | c.*413A>G | 3_prime_UTR_variant | Exon 36 of 36 | ENSP00000518768.1 | |||||
CACNA1H | ENST00000711483.1 | c.*848A>G | 3_prime_UTR_variant | Exon 35 of 35 | ENSP00000518772.1 | |||||
CACNA1H | ENST00000711456.1 | c.*848A>G | 3_prime_UTR_variant | Exon 34 of 34 | ENSP00000518769.1 | |||||
CACNA1H | ENST00000637236.3 | n.*2853A>G | 3_prime_UTR_variant | Exon 34 of 34 | 5 | ENSP00000492650.2 | ||||
CACNA1H | ENST00000639478.1 | n.*1982A>G | 3_prime_UTR_variant | Exon 35 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*4752A>G | 3_prime_UTR_variant | Exon 35 of 35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000711442.1 | n.*6378A>G | 3_prime_UTR_variant | Exon 33 of 34 | ENSP00000518758.1 | |||||
CACNA1H | ENST00000711448.1 | n.*1875A>G | 3_prime_UTR_variant | Exon 36 of 36 | ENSP00000518760.1 | |||||
CACNA1H | ENST00000711449.1 | n.*1793A>G | 3_prime_UTR_variant | Exon 35 of 35 | ENSP00000518761.1 | |||||
CACNA1H | ENST00000711451.1 | n.*2513A>G | 3_prime_UTR_variant | Exon 36 of 36 | ENSP00000518763.1 | |||||
CACNA1H | ENST00000711452.1 | n.*1601A>G | 3_prime_UTR_variant | Exon 36 of 36 | ENSP00000518764.1 | |||||
CACNA1H | ENST00000711453.1 | n.*1568A>G | 3_prime_UTR_variant | Exon 36 of 36 | ENSP00000518765.1 | |||||
CACNA1H | ENST00000711484.1 | n.*848A>G | 3_prime_UTR_variant | Exon 34 of 35 | ENSP00000518773.1 | |||||
CACNA1H | ENST00000711488.1 | n.*2050A>G | 3_prime_UTR_variant | Exon 35 of 35 | ENSP00000518777.1 | |||||
CACNA1H | ENST00000621827.2 | n.6121+813A>G | intron_variant | Intron 35 of 36 | 6 | ENSP00000518766.1 |
Frequencies
GnomAD3 genomes AF: 0.00161 AC: 245AN: 151962Hom.: 3 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00158 AC: 392AN: 248466 AF XY: 0.00159 show subpopulations
GnomAD4 exome AF: 0.00128 AC: 1876AN: 1460482Hom.: 7 Cov.: 34 AF XY: 0.00127 AC XY: 925AN XY: 726540 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00161 AC: 245AN: 152078Hom.: 3 Cov.: 32 AF XY: 0.00173 AC XY: 129AN XY: 74372 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:3
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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CACNA1H: BS1, BS2 -
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at