rs764564753
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_012282.4(KCNE5):c.334G>A(p.Asp112Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000913 in 1,183,360 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012282.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNE5 | NM_012282.4 | c.334G>A | p.Asp112Asn | missense_variant | 1/1 | ENST00000372101.3 | NP_036414.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNE5 | ENST00000372101.3 | c.334G>A | p.Asp112Asn | missense_variant | 1/1 | NM_012282.4 | ENSP00000361173 | P1 | ||
ACSL4 | ENST00000439581.1 | n.387-366G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000709 AC: 8AN: 112891Hom.: 0 Cov.: 25 AF XY: 0.0000854 AC XY: 3AN XY: 35133
GnomAD3 exomes AF: 0.000648 AC: 80AN: 123508Hom.: 0 AF XY: 0.000379 AC XY: 14AN XY: 36968
GnomAD4 exome AF: 0.0000934 AC: 100AN: 1070469Hom.: 0 Cov.: 31 AF XY: 0.0000575 AC XY: 20AN XY: 347859
GnomAD4 genome AF: 0.0000709 AC: 8AN: 112891Hom.: 0 Cov.: 25 AF XY: 0.0000854 AC XY: 3AN XY: 35133
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 18, 2023 | The p.D112N variant (also known as c.334G>A), located in coding exon 1 of the KCNE5 gene, results from a G to A substitution at nucleotide position 334. The aspartic acid at codon 112 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Brugada syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at