rs12554930

Positions:

• chr9-128864561-C-G

Variant summary

Our verdict is Benign. Variant got -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

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-SPOUT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KYAT1	NM_004059.5	c.-7+17336G>C		intron_variant		ENST00000302586.8
KYAT1-SPOUT1	NR_182311.1	n.54+17336G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KYAT1	ENST00000302586.8	c.-7+17336G>C		intron_variant		1	NM_004059.5	P1

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

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.0911

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0770

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.106

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs12554930; hg19: chr9-131626840;