1-88963466-T-C

Variant names:

• chr1-88963466-T-C
• rs1409149
• NM_001008661.3:c.454-1321A>G

Variant summary

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

The NM_001008661.3(KYAT3):​c.454-1321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,060 control chromosomes in the GnomAD database, including 16,373 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 0.46 (16373 hom., cov: 32)
• Consequence: KYAT3 NM_001008661.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 14 publications found

Genes affected

KYAT3 (HGNC:33238): (kynurenine aminotransferase 3) This gene encodes an aminotransferase that transaminates kynurenine to form kynurenic acid, which is a metabolite of tryptophan. Multiple alternatively spliced transcript variants that encode different proteins have been described for this gene. This gene shares 5' exon structure with the RNA binding motif protein, X-linked-like 1 locus on chromosome 1, but the coding sequences are non-overlapping. [provided by RefSeq, Mar 2017]

ENSG00000307240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT3	NM_001008661.3	c.454-1321A>G		intron_variant	Intron 5 of 13	ENST00000260508.9	NP_001008661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KYAT3	ENST00000260508.9	c.454-1321A>G		intron_variant	Intron 5 of 13	1	NM_001008661.3	ENSP00000260508.4

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70151 AN: 151940 Hom.: 16334 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.462 AC: 70237 AN: 152060 Hom.: 16373 Cov.: 32 AF XY: 0.456 AC XY: 33865 AN XY: 74312

African (AFR) AF: 0.412 AC: 17103 AN: 41474

American (AMR) AF: 0.504 AC: 7698 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1424 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2360 AN: 5166

South Asian (SAS) AF: 0.319 AC: 1541 AN: 4824

European-Finnish (FIN) AF: 0.454 AC: 4790 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33698 AN: 67984

Other (OTH) AF: 0.466 AC: 986 AN: 2114

Alfa AF: 0.477 Hom.: 2784

Bravo AF: 0.470

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.52
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs1409149; hg19: chr1-89429149;