17-41842061-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152467.5(KLHL10):āc.433T>Cā(p.Cys145Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,614,166 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 (ā ).
Frequency
Consequence
NM_152467.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHL10 | NM_152467.5 | c.433T>C | p.Cys145Arg | missense_variant | Exon 2 of 5 | ENST00000293303.5 | NP_689680.2 | |
KLHL10 | NM_001329595.1 | c.433T>C | p.Cys145Arg | missense_variant | Exon 4 of 7 | NP_001316524.1 | ||
KLHL10 | NM_001329596.2 | c.169T>C | p.Cys57Arg | missense_variant | Exon 2 of 5 | NP_001316525.1 | ||
KLHL10 | XM_047435897.1 | c.433T>C | p.Cys145Arg | missense_variant | Exon 3 of 6 | XP_047291853.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL10 | ENST00000293303.5 | c.433T>C | p.Cys145Arg | missense_variant | Exon 2 of 5 | 1 | NM_152467.5 | ENSP00000293303.4 | ||
KLHL10 | ENST00000438813.1 | c.415T>C | p.Cys139Arg | missense_variant | Exon 2 of 2 | 4 | ENSP00000416221.1 | |||
KLHL10 | ENST00000485613.1 | n.479T>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249580Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135408
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461892Hom.: 0 Cov.: 35 AF XY: 0.00000550 AC XY: 4AN XY: 727248
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152274Hom.: 0 Cov.: 31 AF XY: 0.0000806 AC XY: 6AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.433T>C (p.C145R) alteration is located in exon 2 (coding exon 2) of the KLHL10 gene. This alteration results from a T to C substitution at nucleotide position 433, causing the cysteine (C) at amino acid position 145 to be replaced by an arginine (R). 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