rs974417
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052904.4(KLHL32):c.24-4275C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,820 control chromosomes in the GnomAD database, including 4,156 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 0.22 ( 4156 hom., cov: 32)
Consequence
KLHL32
NM_052904.4 intron
NM_052904.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.87
Genes affected
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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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL32 | NM_052904.4 | c.24-4275C>T | intron_variant | ENST00000369261.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL32 | ENST00000369261.9 | c.24-4275C>T | intron_variant | 2 | NM_052904.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.219 AC: 33284AN: 151702Hom.: 4153 Cov.: 32
GnomAD3 genomes
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33284
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151702
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.219 AC: 33317AN: 151820Hom.: 4156 Cov.: 32 AF XY: 0.221 AC XY: 16409AN XY: 74222
GnomAD4 genome
?
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33317
AN:
151820
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32
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16409
AN XY:
74222
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Asia WGS
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818
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3478
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