chr14-20429024-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365790.2(KLHL33):c.2219G>A(p.Arg740His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000741 in 1,551,734 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001365790.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL33 | NM_001365790.2 | c.2219G>A | p.Arg740His | missense_variant | 5/5 | ENST00000636854.3 | |
KLHL33 | NM_001109997.3 | c.1427G>A | p.Arg476His | missense_variant | 4/4 | ||
KLHL33 | XM_011536450.3 | c.2219G>A | p.Arg740His | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL33 | ENST00000636854.3 | c.2219G>A | p.Arg740His | missense_variant | 5/5 | 5 | NM_001365790.2 | P1 | |
KLHL33 | ENST00000344581.4 | c.1427G>A | p.Arg476His | missense_variant | 4/4 | 5 | |||
KLHL33 | ENST00000637228.1 | c.*378G>A | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00273 AC: 415AN: 152228Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000854 AC: 133AN: 155668Hom.: 0 AF XY: 0.000727 AC XY: 60AN XY: 82566
GnomAD4 exome AF: 0.000525 AC: 734AN: 1399388Hom.: 2 Cov.: 37 AF XY: 0.000507 AC XY: 350AN XY: 690200
GnomAD4 genome ? AF: 0.00273 AC: 416AN: 152346Hom.: 2 Cov.: 33 AF XY: 0.00260 AC XY: 194AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | KLHL33: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at