rs786205259
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PVS1_ModerateBS2
The NM_005477.3(HCN4):c.3502_3505delTTTG(p.Phe1168GlyfsTer12) variant causes a frameshift change. The variant allele was found at a frequency of 0.000112 in 1,610,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005477.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000108 AC: 26AN: 240632Hom.: 0 AF XY: 0.0000841 AC XY: 11AN XY: 130768
GnomAD4 exome AF: 0.000104 AC: 152AN: 1458350Hom.: 0 AF XY: 0.0000883 AC XY: 64AN XY: 725078
GnomAD4 genome AF: 0.000184 AC: 28AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74288
ClinVar
Submissions by phenotype
not provided Uncertain:5
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Reported in an individual in the ClinSeq Project who had a normal ECG and echocardiogram and no family history of arrhythmia or sudden cardiac death; denoted as c.3498_3501del due to alternate nomenclature (Ng et al., 2013); Has been reported as a variant of uncertain significance in an individual with Brugada syndrome (Sarquella-Brugada et al., 2021); Frameshift variant predicted to result in protein truncation as the last 36 amino acids are replaced with 11 different amino acids; This variant is associated with the following publications: (PMID: 26046366, 26582918, 23861362, 34546463) -
Sinoatrial node disorder Uncertain:1
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Sick sinus syndrome 2, autosomal dominant;C2751083:Brugada syndrome 8;C5561983:Epilepsy, idiopathic generalized, susceptibility to, 18 Uncertain:1
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Brugada syndrome 8 Uncertain:1
This sequence change creates a premature translational stop signal (p.Phe1168Glyfs*12) in the HCN4 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 36 amino acid(s) of the HCN4 protein. This variant is present in population databases (rs771725926, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with sinus node disease (PMID: 23861362). ClinVar contains an entry for this variant (Variation ID: 191377). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Cardiovascular phenotype Uncertain:1
The c.3502_3505delTTTG variant, located in coding exon 8 of the HCN4 gene, results from a deletion of 4 nucleotides at nucleotide positions 3502 to 3505, causing a translational frameshift with a predicted alternate stop codon (p.F1168Gfs*12). This variant has been detected in individuals reported to have Brugada syndrome and atrial fibrillation; however, clinical details were limited and additional variants in arrhythmia-associated genes were detected in some cases (van Lint FHM et al. Neth Heart J. 2019 Jun;27(6):304-309; Sarquella-Brugada G et al. Hum Genet, 2022 Oct;141(10):1579-1589). This alteration is expected to result in protein truncation or nonsense-mediated mRNA decay. However, loss of function of HCN4 has not been established as a mechanism of disease. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at