rs10988134

chr9-128833128-C-T

Variant summary

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

The NM_004059.5(KYAT1):c.*456G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 172,850 control chromosomes in the GnomAD database, including 11,108 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 0.34 (10555 hom., cov: 31)
  • Exomes 𝑓: 0.20 (553 hom.)
• Consequence: KYAT1 NM_004059.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KYAT1	NM_004059.5	c.*456G>A		3_prime_UTR_variant	13/13	ENST00000302586.8
KYAT1-SPOUT1	NR_182311.1	n.1686+99G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KYAT1	ENST00000302586.8	c.*456G>A		3_prime_UTR_variant	13/13	1	NM_004059.5	P1
KYAT1	ENST00000462722.5	n.1903G>A		non_coding_transcript_exon_variant	13/13	1
KYAT1	ENST00000320665.10	c.*456G>A		3_prime_UTR_variant	12/12	2
KYAT1	ENST00000483599.5	n.2485G>A		non_coding_transcript_exon_variant	13/13	2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51521 AN: 151720 Hom.: 10544 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.200 AC: 4198 AN: 21012 Hom.: 553 Cov.: 0 AF XY: 0.207 AC XY: 2209 AN XY: 10656

Gnomad4 AFR exome AF: 0.494

Gnomad4 AMR exome AF: 0.178

Gnomad4 ASJ exome AF: 0.171

Gnomad4 EAS exome AF: 0.194

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.121

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.212

GnomAD4 genome AF: 0.340 AC: 51577 AN: 151838 Hom.: 10555 Cov.: 31 AF XY: 0.335 AC XY: 24842 AN XY: 74202

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.328

Alfa AF: 0.269 Hom.: 7784

Bravo AF: 0.352

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	2.1
Dann	Benign	0.77

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: rs10988134; hg19: chr9-131595407;