chr5-45695884-G-GCCGCCGCCA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM4BP6_Very_StrongBS2
The NM_021072.4(HCN1):c.201_209dupTGGCGGCGG(p.Gly68_Gly70dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000163 in 1,529,784 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021072.4 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCN1 | ENST00000303230.6 | c.201_209dupTGGCGGCGG | p.Gly68_Gly70dup | disruptive_inframe_insertion | Exon 1 of 8 | 1 | NM_021072.4 | ENSP00000307342.4 | ||
HCN1 | ENST00000673735.1 | c.201_209dupTGGCGGCGG | p.Gly68_Gly70dup | disruptive_inframe_insertion | Exon 1 of 9 | ENSP00000501107.1 | ||||
HCN1 | ENST00000634658.1 | c.201_209dupTGGCGGCGG | p.Gly68_Gly70dup | disruptive_inframe_insertion | Exon 1 of 2 | 3 | ENSP00000489134.1 |
Frequencies
GnomAD3 genomes AF: 0.000179 AC: 27AN: 150518Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000162 AC: 223AN: 1379162Hom.: 0 Cov.: 33 AF XY: 0.000167 AC XY: 114AN XY: 681952
GnomAD4 genome AF: 0.000179 AC: 27AN: 150622Hom.: 0 Cov.: 32 AF XY: 0.000163 AC XY: 12AN XY: 73604
ClinVar
Submissions by phenotype
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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not provided Benign:1
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Intellectual disability Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at