17-41845328-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_152467.5(KLHL10):c.887T>C(p.Ile296Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00797 in 1,614,174 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_152467.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHL10 | NM_152467.5 | c.887T>C | p.Ile296Thr | missense_variant | Exon 3 of 5 | ENST00000293303.5 | NP_689680.2 | |
KLHL10 | NM_001329595.1 | c.887T>C | p.Ile296Thr | missense_variant | Exon 5 of 7 | NP_001316524.1 | ||
KLHL10 | NM_001329596.2 | c.623T>C | p.Ile208Thr | missense_variant | Exon 3 of 5 | NP_001316525.1 | ||
KLHL10 | XM_047435897.1 | c.887T>C | p.Ile296Thr | missense_variant | Exon 4 of 6 | XP_047291853.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00559 AC: 850AN: 152188Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00546 AC: 1361AN: 249422Hom.: 5 AF XY: 0.00550 AC XY: 744AN XY: 135322
GnomAD4 exome AF: 0.00822 AC: 12014AN: 1461868Hom.: 75 Cov.: 32 AF XY: 0.00789 AC XY: 5739AN XY: 727232
GnomAD4 genome AF: 0.00558 AC: 850AN: 152306Hom.: 4 Cov.: 32 AF XY: 0.00485 AC XY: 361AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
KLHL10: PP2, BS2 -
- -
Non-obstructive azoospermia Uncertain:1
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KLHL10-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at