rs17133163
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014997.4(KLHDC10):c.253+1604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,038 control chromosomes in the GnomAD database, including 6,054 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: 𝑓 0.27 ( 6054 hom., cov: 32)
Consequence
KLHDC10
NM_014997.4 intron
NM_014997.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.862
Genes affected
KLHDC10 (HGNC:22194): (kelch domain containing 10) Enables ubiquitin ligase-substrate adaptor activity. Involved in ubiquitin-dependent protein catabolic process via the C-end degron rule pathway. Located in nucleoplasm. Is active in Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHDC10 | NM_014997.4 | c.253+1604T>C | intron_variant | ENST00000335420.10 | NP_055812.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHDC10 | ENST00000335420.10 | c.253+1604T>C | intron_variant | 1 | NM_014997.4 | ENSP00000334140.4 | ||||
KLHDC10 | ENST00000468226.1 | c.-177+1604T>C | intron_variant | 3 | ENSP00000420034.1 | |||||
KLHDC10 | ENST00000463413.1 | c.167-17834T>C | intron_variant | 2 | ENSP00000420083.1 |
Frequencies
GnomAD3 genomes AF: 0.269 AC: 40814AN: 151920Hom.: 6048 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.269 AC: 40851AN: 152038Hom.: 6054 Cov.: 32 AF XY: 0.266 AC XY: 19764AN XY: 74320
GnomAD4 genome
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19764
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375
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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