rs771120157
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_139318.5(KCNH5):c.1569+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,609,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_139318.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH5 | NM_139318.5 | c.1569+7G>T | splice_region_variant, intron_variant | ENST00000322893.12 | |||
KCNH5 | NM_172375.3 | c.1569+7G>T | splice_region_variant, intron_variant | ||||
KCNH5 | XM_047431275.1 | c.1569+7G>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH5 | ENST00000322893.12 | c.1569+7G>T | splice_region_variant, intron_variant | 1 | NM_139318.5 | P1 | |||
KCNH5 | ENST00000420622.6 | c.1569+7G>T | splice_region_variant, intron_variant | 1 | |||||
KCNH5 | ENST00000394968.2 | c.1395+7G>T | splice_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250880Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135600
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1457284Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 725294
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74278
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 27, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at