rs941960

Variant names:

• chr9-128878753-C-G
• rs941960
• NM_004059.5:c.-7+3144G>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+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
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004059.5. 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.-7+3144G>C		intron	N/A	NP_004050.3
	KYAT1-SPOUT1	NM_001414398.1		c.-7+3150G>C		intron	N/A	NP_001401327.1
	KYAT1	NM_001287390.3		c.-116+3144G>C		intron	N/A	NP_001274319.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KYAT1	ENST00000302586.8	TSL:1 MANE Select	c.-7+3144G>C		intron	N/A	ENSP00000302227.3
	KYAT1	ENST00000651925.1		c.-116+3144G>C		intron	N/A	ENSP00000498386.1
	KYAT1	ENST00000462722.5	TSL:1	n.140+3144G>C		intron	N/A

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

African (AFR) AF: 0.386 AC: 15979 AN: 41430

American (AMR) AF: 0.752 AC: 11462 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2522 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3725 AN: 5148

South Asian (SAS) AF: 0.610 AC: 2946 AN: 4826

European-Finnish (FIN) AF: 0.785 AC: 8298 AN: 10574

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47945 AN: 67958

Other (OTH) AF: 0.654 AC: 1377 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.35

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

Other links and lift over

dbSNP: rs941960; hg19: chr9-131641032;