chr17-63533915-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001278919.2(KCNH6):c.705G>A(p.Pro235=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000615 in 1,613,720 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00059 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00062 ( 6 hom. )
Consequence
KCNH6
NM_001278919.2 synonymous
NM_001278919.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -8.03
Genes affected
KCNH6 (HGNC:18862): (potassium voltage-gated channel subfamily H member 6) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, subfamily H. This member is a pore-forming (alpha) subunit. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 17-63533915-G-A is Benign according to our data. Variant chr17-63533915-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648079.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-8.03 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH6 | NM_001278919.2 | c.705G>A | p.Pro235= | synonymous_variant | 5/13 | ENST00000314672.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH6 | ENST00000314672.10 | c.705G>A | p.Pro235= | synonymous_variant | 5/13 | 2 | NM_001278919.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000598 AC: 91AN: 152110Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000990 AC: 248AN: 250544Hom.: 0 AF XY: 0.000946 AC XY: 128AN XY: 135360
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GnomAD4 exome AF: 0.000618 AC: 903AN: 1461492Hom.: 6 Cov.: 31 AF XY: 0.000653 AC XY: 475AN XY: 727014
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GnomAD4 genome ? AF: 0.000591 AC: 90AN: 152228Hom.: 1 Cov.: 32 AF XY: 0.000511 AC XY: 38AN XY: 74432
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | KCNH6: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at