16-1216940-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_021098.3(CACNA1H):c.5253C>T(p.Asn1751Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00209 in 1,602,734 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021098.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.5253C>T | p.Asn1751Asn | synonymous_variant | Exon 31 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.5235C>T | p.Asn1745Asn | synonymous_variant | Exon 29 of 33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.5214C>T | p.Asn1738Asn | synonymous_variant | Exon 31 of 35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000569107.5 | c.1491C>T | p.Asn497Asn | synonymous_variant | Exon 13 of 17 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000564231.5 | c.1476C>T | p.Asn492Asn | synonymous_variant | Exon 14 of 18 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000562079.5 | c.1458C>T | p.Asn486Asn | synonymous_variant | Exon 13 of 17 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000639478.1 | n.*334C>T | non_coding_transcript_exon_variant | Exon 31 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*3104C>T | non_coding_transcript_exon_variant | Exon 31 of 35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000639478.1 | n.*334C>T | 3_prime_UTR_variant | Exon 31 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*3104C>T | 3_prime_UTR_variant | Exon 31 of 35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.00174 AC: 265AN: 152198Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00170 AC: 384AN: 226014Hom.: 1 AF XY: 0.00178 AC XY: 219AN XY: 123084
GnomAD4 exome AF: 0.00213 AC: 3084AN: 1450418Hom.: 9 Cov.: 31 AF XY: 0.00216 AC XY: 1559AN XY: 720420
GnomAD4 genome AF: 0.00174 AC: 265AN: 152316Hom.: 1 Cov.: 34 AF XY: 0.00165 AC XY: 123AN XY: 74480
ClinVar
Submissions by phenotype
CACNA1H-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Epilepsy, childhood absence, susceptibility to, 6;C4310756:Hyperaldosteronism, familial, type IV Benign:1
- -
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
- -
not provided Benign:1
CACNA1H: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at