chr5-45695884-GCCGCCGCCA-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1
The NM_021072.4(HCN1):c.201_209delTGGCGGCGG(p.Gly68_Gly70del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,529,748 control chromosomes in the GnomAD database, including 621 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_021072.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCN1 | ENST00000303230.6 | c.201_209delTGGCGGCGG | p.Gly68_Gly70del | disruptive_inframe_deletion | Exon 1 of 8 | 1 | NM_021072.4 | ENSP00000307342.4 | ||
HCN1 | ENST00000673735.1 | c.201_209delTGGCGGCGG | p.Gly68_Gly70del | disruptive_inframe_deletion | Exon 1 of 9 | ENSP00000501107.1 | ||||
HCN1 | ENST00000634658.1 | c.201_209delTGGCGGCGG | p.Gly68_Gly70del | disruptive_inframe_deletion | Exon 1 of 2 | 3 | ENSP00000489134.1 |
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 4277AN: 150482Hom.: 87 Cov.: 32
GnomAD3 exomes AF: 0.0198 AC: 2842AN: 143504Hom.: 140 AF XY: 0.0205 AC XY: 1633AN XY: 79598
GnomAD4 exome AF: 0.0204 AC: 28203AN: 1379162Hom.: 534 AF XY: 0.0205 AC XY: 14004AN XY: 681950
GnomAD4 genome AF: 0.0284 AC: 4280AN: 150586Hom.: 87 Cov.: 32 AF XY: 0.0264 AC XY: 1942AN XY: 73588
ClinVar
Submissions by phenotype
not provided Benign:2
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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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at