rs35141484
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_015990.5(KLHL5):āc.1107A>Cā(p.Ala369=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00393 in 1,611,014 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.021 ( 116 hom., cov: 32)
Exomes š: 0.0022 ( 104 hom. )
Consequence
KLHL5
NM_015990.5 synonymous
NM_015990.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.33
Genes affected
KLHL5 (HGNC:6356): (kelch like family member 5) Predicted to enable actin binding activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP7
?
Synonymous conserved (PhyloP=-1.33 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0686 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL5 | NM_015990.5 | c.1107A>C | p.Ala369= | synonymous_variant | 5/11 | ENST00000504108.7 | |
LOC105374418 | XR_925235.4 | n.66+9033T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL5 | ENST00000504108.7 | c.1107A>C | p.Ala369= | synonymous_variant | 5/11 | 2 | NM_015990.5 | A1 | |
ENST00000668468.1 | n.270-17587T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0203 AC: 3093AN: 152106Hom.: 111 Cov.: 32
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GnomAD3 exomes AF: 0.00555 AC: 1393AN: 250842Hom.: 46 AF XY: 0.00397 AC XY: 538AN XY: 135556
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GnomAD4 exome AF: 0.00220 AC: 3205AN: 1458790Hom.: 104 Cov.: 29 AF XY: 0.00192 AC XY: 1397AN XY: 725926
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GnomAD4 genome ? AF: 0.0205 AC: 3124AN: 152224Hom.: 116 Cov.: 32 AF XY: 0.0196 AC XY: 1461AN XY: 74436
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at