rs55978915
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001194.4(HCN2):c.1584+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 1,611,018 control chromosomes in the GnomAD database, including 293 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001194.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HCN2 | NM_001194.4 | c.1584+7C>T | splice_region_variant, intron_variant | ENST00000251287.3 | NP_001185.3 | |||
LOC107987266 | XR_001753828.2 | n.1338G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCN2 | ENST00000251287.3 | c.1584+7C>T | splice_region_variant, intron_variant | 1 | NM_001194.4 | ENSP00000251287.1 |
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 1932AN: 152174Hom.: 22 Cov.: 33
GnomAD3 exomes AF: 0.0139 AC: 3431AN: 247182Hom.: 31 AF XY: 0.0134 AC XY: 1799AN XY: 134340
GnomAD4 exome AF: 0.0176 AC: 25670AN: 1458726Hom.: 271 Cov.: 32 AF XY: 0.0171 AC XY: 12377AN XY: 725686
GnomAD4 genome AF: 0.0127 AC: 1932AN: 152292Hom.: 22 Cov.: 33 AF XY: 0.0127 AC XY: 946AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 25, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 168/13002=1.2% - |
HCN2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at