rs11545829
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000171111.10(KEAP1):c.1611C>T(p.Tyr537=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 1,613,870 control chromosomes in the GnomAD database, including 2,481 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 0.020 ( 266 hom., cov: 31)
Exomes 𝑓: 0.016 ( 2215 hom. )
Consequence
KEAP1
ENST00000171111.10 synonymous
ENST00000171111.10 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.263
Genes affected
KEAP1 (HGNC:23177): (kelch like ECH associated protein 1) This gene encodes a protein containing KELCH-1 like domains, as well as a BTB/POZ domain. Kelch-like ECH-associated protein 1 interacts with NF-E2-related factor 2 in a redox-sensitive manner and the dissociation of the proteins in the cytoplasm is followed by transportation of NF-E2-related factor 2 to the nucleus. This interaction results in the expression of the catalytic subunit of gamma-glutamylcysteine synthetase. Two alternatively spliced transcript variants encoding the same isoform have been found for this gene. [provided by RefSeq, Jul 2008]
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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=-0.56).
BP7
Synonymous conserved (PhyloP=-0.263 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KEAP1 | NM_203500.2 | c.1611C>T | p.Tyr537= | synonymous_variant | 5/6 | ENST00000171111.10 | NP_987096.1 | |
KEAP1 | NM_012289.4 | c.1611C>T | p.Tyr537= | synonymous_variant | 5/6 | NP_036421.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KEAP1 | ENST00000171111.10 | c.1611C>T | p.Tyr537= | synonymous_variant | 5/6 | 1 | NM_203500.2 | ENSP00000171111 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0204 AC: 3096AN: 151938Hom.: 265 Cov.: 31
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GnomAD3 exomes AF: 0.0416 AC: 10465AN: 251306Hom.: 951 AF XY: 0.0390 AC XY: 5297AN XY: 135854
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GnomAD4 exome AF: 0.0156 AC: 22857AN: 1461814Hom.: 2215 Cov.: 33 AF XY: 0.0163 AC XY: 11861AN XY: 727208
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GnomAD4 genome AF: 0.0204 AC: 3109AN: 152056Hom.: 266 Cov.: 31 AF XY: 0.0229 AC XY: 1702AN XY: 74322
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at