rs10496935
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003937.3(KYNU):c.902+2904C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,558,488 control chromosomes in the GnomAD database, including 42,147 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 0.26 ( 5799 hom., cov: 32)
Exomes 𝑓: 0.22 ( 36348 hom. )
Consequence
KYNU
NM_003937.3 intron
NM_003937.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0970
Genes affected
KYNU (HGNC:6469): (kynureninase) Kynureninase is a pyridoxal-5'-phosphate (pyridoxal-P) dependent enzyme that catalyzes the cleavage of L-kynurenine and L-3-hydroxykynurenine into anthranilic and 3-hydroxyanthranilic acids, respectively. Kynureninase is involved in the biosynthesis of NAD cofactors from tryptophan through the kynurenine pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2010]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KYNU | NM_003937.3 | c.902+2904C>G | intron_variant | ENST00000264170.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KYNU | ENST00000264170.9 | c.902+2904C>G | intron_variant | 1 | NM_003937.3 | P1 | |||
KYNU | ENST00000375773.6 | c.*38+21C>G | intron_variant | 1 | |||||
KYNU | ENST00000409512.5 | c.902+2904C>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.262 AC: 39670AN: 151616Hom.: 5787 Cov.: 32
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GnomAD4 exome AF: 0.217 AC: 305547AN: 1406754Hom.: 36348 Cov.: 24 AF XY: 0.221 AC XY: 155111AN XY: 702846
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GnomAD4 genome ? AF: 0.262 AC: 39713AN: 151734Hom.: 5799 Cov.: 32 AF XY: 0.264 AC XY: 19611AN XY: 74156
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at