rs142252600
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_139318.5(KCNH5):āc.528T>Cā(p.His176=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000661 in 1,613,086 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00047 ( 0 hom., cov: 33)
Exomes š: 0.00068 ( 1 hom. )
Consequence
KCNH5
NM_139318.5 synonymous
NM_139318.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.05
Genes affected
KCNH5 (HGNC:6254): (potassium voltage-gated channel subfamily H member 5) This gene encodes a member of voltage-gated potassium channels. Members of this family have diverse functions, including regulating neurotransmitter and hormone release, cardiac function, and cell volume. This protein is an outward-rectifying, noninactivating channel. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 14-62987093-A-G is Benign according to our data. Variant chr14-62987093-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 416116.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd4 at 72 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH5 | NM_139318.5 | c.528T>C | p.His176= | synonymous_variant | 5/11 | ENST00000322893.12 | |
KCNH5 | NM_172375.3 | c.528T>C | p.His176= | synonymous_variant | 5/10 | ||
KCNH5 | XM_047431275.1 | c.528T>C | p.His176= | synonymous_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH5 | ENST00000322893.12 | c.528T>C | p.His176= | synonymous_variant | 5/11 | 1 | NM_139318.5 | P1 | |
KCNH5 | ENST00000420622.6 | c.528T>C | p.His176= | synonymous_variant | 5/10 | 1 | |||
KCNH5 | ENST00000394964.3 | n.693T>C | non_coding_transcript_exon_variant | 5/7 | 1 | ||||
KCNH5 | ENST00000394968.2 | c.354T>C | p.His118= | synonymous_variant | 5/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152196Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000275 AC: 69AN: 251244Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135776
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GnomAD4 exome AF: 0.000680 AC: 994AN: 1460890Hom.: 1 Cov.: 30 AF XY: 0.000676 AC XY: 491AN XY: 726824
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GnomAD4 genome ? AF: 0.000473 AC: 72AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74352
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at