3-47330118-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_025010.5(KLHL18):c.569G>A(p.Arg190Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025010.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHL18 | NM_025010.5 | c.569G>A | p.Arg190Gln | missense_variant | 4/10 | ENST00000232766.6 | NP_079286.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL18 | ENST00000232766.6 | c.569G>A | p.Arg190Gln | missense_variant | 4/10 | 1 | NM_025010.5 | ENSP00000232766.5 | ||
KLHL18 | ENST00000442272.1 | n.*258G>A | non_coding_transcript_exon_variant | 3/9 | 2 | ENSP00000392507.1 | ||||
KLHL18 | ENST00000461084.5 | n.589G>A | non_coding_transcript_exon_variant | 4/7 | 2 | |||||
KLHL18 | ENST00000442272.1 | n.*258G>A | 3_prime_UTR_variant | 3/9 | 2 | ENSP00000392507.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251392Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135876
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727238
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.569G>A (p.R190Q) alteration is located in exon 4 (coding exon 4) of the KLHL18 gene. This alteration results from a G to A substitution at nucleotide position 569, causing the arginine (R) at amino acid position 190 to be replaced by a glutamine (Q). 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