3-42686490-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_152393.4(KLHL40):āc.872A>Cā(p.Lys291Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00197 in 1,614,126 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_152393.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL40 | NM_152393.4 | c.872A>C | p.Lys291Thr | missense_variant | 1/6 | ENST00000287777.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL40 | ENST00000287777.5 | c.872A>C | p.Lys291Thr | missense_variant | 1/6 | 1 | NM_152393.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00237 AC: 361AN: 152188Hom.: 10 Cov.: 33
GnomAD3 exomes AF: 0.00546 AC: 1371AN: 251198Hom.: 30 AF XY: 0.00494 AC XY: 670AN XY: 135746
GnomAD4 exome AF: 0.00192 AC: 2811AN: 1461820Hom.: 68 Cov.: 30 AF XY: 0.00185 AC XY: 1344AN XY: 727200
GnomAD4 genome AF: 0.00238 AC: 362AN: 152306Hom.: 10 Cov.: 33 AF XY: 0.00281 AC XY: 209AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 20, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Nemaline myopathy 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at