9-128845642-A-T

Variant names:

• chr9-128845642-A-T
• rs2259043
• NM_004059.5:c.-6-231T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001352993.2(KYAT1):​c.-44T>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KYAT1 NM_001352993.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• Publications: 16 publications found

Genes affected

KYAT1 (HGNC:1564): (kynurenine aminotransferase 1) This gene encodes a cytosolic enzyme that is responsible for the metabolism of cysteine conjugates of certain halogenated alkenes and alkanes. This metabolism can form reactive metabolites leading to nephrotoxicity and neurotoxicity. Increased levels of this enzyme have been linked to schizophrenia. Multiple transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

KYAT1 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352993.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KYAT1	NM_004059.5	MANE Select	c.-6-231T>A		intron	N/A	NP_004050.3
	KYAT1	NM_001352993.2		c.-44T>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 13	NP_001339922.1	Q16773-1
	KYAT1	NM_001352993.2		c.-44T>A		5_prime_UTR	Exon 1 of 13	NP_001339922.1	Q16773-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KYAT1	ENST00000302586.8	TSL:1 MANE Select	c.-6-231T>A		intron	N/A	ENSP00000302227.3	Q16773-1
	KYAT1	ENST00000651925.1		c.274-231T>A		intron	N/A	ENSP00000498386.1	A0A494C066
	KYAT1	ENST00000462722.5	TSL:1	n.141-231T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 385286 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 204586

African (AFR) AF: 0.00 AC: 0 AN: 9838

American (AMR) AF: 0.00 AC: 0 AN: 15552

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11660

East Asian (EAS) AF: 0.00 AC: 0 AN: 24582

South Asian (SAS) AF: 0.00 AC: 0 AN: 43862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24472

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1670

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 231660

Other (OTH) AF: 0.00 AC: 0 AN: 21990

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.86
PhyloP100		-0.90
PromoterAI		0.054	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.16		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2259043; hg19: chr9-131607921;