rs12554930

Variant names:

• chr9-128864561-C-G
• rs12554930
• NM_004059.5:c.-7+17336G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004059.5(KYAT1):​c.-7+17336G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,998 control chromosomes in the GnomAD database, including 1,072 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 0.11 (1072 hom., cov: 29)
• Consequence: KYAT1 NM_004059.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT1	NM_004059.5	c.-7+17336G>C		intron_variant	Intron 1 of 12	ENST00000302586.8	NP_004050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KYAT1	ENST00000302586.8	c.-7+17336G>C		intron_variant	Intron 1 of 12	1	NM_004059.5	ENSP00000302227.3
KYAT1	ENST00000651925.1	c.-115-16918G>C		intron_variant	Intron 1 of 28			ENSP00000498386.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16229 AN: 151880 Hom.: 1070 Cov.: 29

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.101

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16242 AN: 151998 Hom.: 1072 Cov.: 29 AF XY: 0.105 AC XY: 7803 AN XY: 74308

African (AFR) AF: 0.0410 AC: 1699 AN: 41470

American (AMR) AF: 0.0911 AC: 1390 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3472

East Asian (EAS) AF: 0.0770 AC: 397 AN: 5154

South Asian (SAS) AF: 0.168 AC: 810 AN: 4810

European-Finnish (FIN) AF: 0.102 AC: 1075 AN: 10554

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9931 AN: 67966

Other (OTH) AF: 0.106 AC: 223 AN: 2108

Alfa AF: 0.126 Hom.: 177

Bravo AF: 0.101

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		0.27
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs12554930; hg19: chr9-131626840;