rs941960

Variant names:

• chr9-128878753-C-G
• rs941960
• NM_004059.5:c.-7+3144G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004059.5(KYAT1):​c.-7+3144G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,964 control chromosomes in the GnomAD database, including 31,622 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 0.63 (31622 hom., cov: 30)
• Consequence: KYAT1 NM_004059.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

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]

ENSG00000286112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT1	NM_004059.5	c.-7+3144G>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+3144G>C		intron_variant	Intron 1 of 12	1	NM_004059.5	ENSP00000302227.3
ENSG00000286112	ENST00000651925.1	c.-116+3144G>C		intron_variant	Intron 1 of 28			ENSP00000498386.1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95110 AN: 151846 Hom.: 31612 Cov.: 30

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.626 AC: 95163 AN: 151964 Hom.: 31622 Cov.: 30 AF XY: 0.634 AC XY: 47062 AN XY: 74258

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.654

Alfa AF: 0.657 Hom.: 4216

Bravo AF: 0.618

Asia WGS AF: 0.655 AC: 2276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs941960; hg19: chr9-131641032;