rs56154381
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_021072.4(HCN1):c.1783+7_1783+8insT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,607,762 control chromosomes in the GnomAD database, including 862 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.046 ( 448 hom., cov: 31)
Exomes 𝑓: 0.0098 ( 414 hom. )
Consequence
HCN1
NM_021072.4 splice_region, intron
NM_021072.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.222
Genes affected
HCN1 (HGNC:4845): (hyperpolarization activated cyclic nucleotide gated potassium channel 1) The membrane protein encoded by this gene is a hyperpolarization-activated cation channel that contributes to the native pacemaker currents in heart and neurons. The encoded protein can homodimerize or heterodimerize with other pore-forming subunits to form a potassium channel. This channel may act as a receptor for sour tastes. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 5-45267081-T-TA is Benign according to our data. Variant chr5-45267081-T-TA is described in ClinVar as [Benign]. Clinvar id is 198584.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCN1 | NM_021072.4 | c.1783+7_1783+8insT | splice_region_variant, intron_variant | ENST00000303230.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCN1 | ENST00000303230.6 | c.1783+7_1783+8insT | splice_region_variant, intron_variant | 1 | NM_021072.4 | P2 | |||
HCN1 | ENST00000673735.1 | c.1783+7_1783+8insT | splice_region_variant, intron_variant | A2 | |||||
HCN1 | ENST00000637305.1 | n.946+7_946+8insT | splice_region_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0460 AC: 6991AN: 152060Hom.: 441 Cov.: 31
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GnomAD3 exomes AF: 0.0162 AC: 4074AN: 251488Hom.: 188 AF XY: 0.0136 AC XY: 1854AN XY: 135918
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GnomAD4 exome AF: 0.00982 AC: 14299AN: 1455584Hom.: 414 Cov.: 28 AF XY: 0.00954 AC XY: 6912AN XY: 724692
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GnomAD4 genome AF: 0.0462 AC: 7030AN: 152178Hom.: 448 Cov.: 31 AF XY: 0.0452 AC XY: 3365AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 26, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 26, 2015 | - - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 18, 2021 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at