rs3752158
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001194.4(HCN2):c.1239G>A(p.Leu413=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,612,242 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L413L) has been classified as Benign.
Frequency
Consequence
NM_001194.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCN2 | NM_001194.4 | c.1239G>A | p.Leu413= | synonymous_variant | 4/8 | ENST00000251287.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCN2 | ENST00000251287.3 | c.1239G>A | p.Leu413= | synonymous_variant | 4/8 | 1 | NM_001194.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000874 AC: 133AN: 152184Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00150 AC: 373AN: 248694Hom.: 3 AF XY: 0.00196 AC XY: 264AN XY: 135008
GnomAD4 exome AF: 0.00118 AC: 1729AN: 1459940Hom.: 19 Cov.: 32 AF XY: 0.00141 AC XY: 1022AN XY: 726298
GnomAD4 genome ? AF: 0.000880 AC: 134AN: 152302Hom.: 1 Cov.: 33 AF XY: 0.000954 AC XY: 71AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at