rs202198564
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000238.4(KCNH2):c.3279G>T(p.Pro1093Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,598,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000238.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNH2 | NM_000238.4 | c.3279G>T | p.Pro1093Pro | synonymous_variant | 14/15 | ENST00000262186.10 | NP_000229.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNH2 | ENST00000262186.10 | c.3279G>T | p.Pro1093Pro | synonymous_variant | 14/15 | 1 | NM_000238.4 | ENSP00000262186.5 | ||
KCNH2 | ENST00000330883.9 | c.2259G>T | p.Pro753Pro | synonymous_variant | 10/11 | 1 | ENSP00000328531.4 | |||
KCNH2 | ENST00000684241.1 | n.4112G>T | non_coding_transcript_exon_variant | 12/13 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151828Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242262Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130552
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1446132Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 717202
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151946Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74282
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at