chr2-169510641-T-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP3BP4_StrongBP6_Very_StrongBS1BS2
The NM_006063.3(KLHL41):āc.863T>Gā(p.Leu288Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00767 in 1,614,174 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_006063.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL41 | ENST00000284669.2 | c.863T>G | p.Leu288Arg | missense_variant | Exon 1 of 6 | 1 | NM_006063.3 | ENSP00000284669.1 | ||
ENSG00000251569 | ENST00000513963.1 | c.925-3933T>G | intron_variant | Intron 11 of 15 | 2 | ENSP00000424363.1 |
Frequencies
GnomAD3 genomes AF: 0.00568 AC: 864AN: 152170Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00556 AC: 1398AN: 251464Hom.: 10 AF XY: 0.00554 AC XY: 753AN XY: 135912
GnomAD4 exome AF: 0.00787 AC: 11512AN: 1461886Hom.: 92 Cov.: 33 AF XY: 0.00765 AC XY: 5563AN XY: 727244
GnomAD4 genome AF: 0.00567 AC: 864AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.00561 AC XY: 418AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:3
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KLHL41: BS2 -
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not specified Benign:2
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Nemaline myopathy 9 Benign:2
This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at