chr2-142885490-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_003937.3(KYNU):c.123C>T(p.His41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,613,930 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0096 ( 26 hom., cov: 29)
Exomes 𝑓: 0.0012 ( 24 hom. )
Consequence
KYNU
NM_003937.3 synonymous
NM_003937.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.566
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 2-142885490-C-T is Benign according to our data. Variant chr2-142885490-C-T is described in ClinVar as [Benign]. Clinvar id is 785012.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.566 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00962 (1464/152220) while in subpopulation AFR AF= 0.0328 (1362/41524). AF 95% confidence interval is 0.0314. There are 26 homozygotes in gnomad4. There are 706 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KYNU | NM_003937.3 | c.123C>T | p.His41= | synonymous_variant | 2/14 | ENST00000264170.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KYNU | ENST00000264170.9 | c.123C>T | p.His41= | synonymous_variant | 2/14 | 1 | NM_003937.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00959 AC: 1459AN: 152102Hom.: 26 Cov.: 29
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GnomAD3 exomes AF: 0.00259 AC: 652AN: 251468Hom.: 17 AF XY: 0.00202 AC XY: 274AN XY: 135918
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GnomAD4 exome AF: 0.00121 AC: 1762AN: 1461710Hom.: 24 Cov.: 31 AF XY: 0.00105 AC XY: 762AN XY: 727136
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GnomAD4 genome ? AF: 0.00962 AC: 1464AN: 152220Hom.: 26 Cov.: 29 AF XY: 0.00949 AC XY: 706AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at