chr2-23642562-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_052920.2(KLHL29):c.652G>A(p.Val218Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,396,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052920.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL29 | NM_052920.2 | c.652G>A | p.Val218Met | missense_variant | 5/14 | ENST00000486442.6 | |
KLHL29 | XM_006711929.4 | c.652G>A | p.Val218Met | missense_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL29 | ENST00000486442.6 | c.652G>A | p.Val218Met | missense_variant | 5/14 | 5 | NM_052920.2 | P1 | |
KLHL29 | ENST00000288548.5 | c.172G>A | p.Val58Met | missense_variant | 1/7 | 1 | |||
KLHL29 | ENST00000489446.1 | n.733G>A | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.16e-7 AC: 1AN: 1396616Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 688486
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.652G>A (p.V218M) alteration is located in exon 5 (coding exon 3) of the KLHL29 gene. This alteration results from a G to A substitution at nucleotide position 652, causing the valine (V) at amino acid position 218 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.