rs10922530

Positions:

• chr1-88961569-G-A

Variant summary

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

The NM_001008661.3(KYAT3):​c.541-63C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 1,388,048 control chromosomes in the GnomAD database, including 96,630 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 0.31 (8326 hom., cov: 32)
  • Exomes 𝑓: 0.37 (88304 hom.)
• Consequence: KYAT3 NM_001008661.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

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]

KYAT3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KYAT3	NM_001008661.3	c.541-63C>T		intron_variant		ENST00000260508.9	NP_001008661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KYAT3	ENST00000260508.9	c.541-63C>T		intron_variant		1	NM_001008661.3	ENSP00000260508.4
KYAT3	ENST00000370491.7	c.439-63C>T		intron_variant		2		ENSP00000359522.3
KYAT3	ENST00000370486.1	c.541-63C>T		intron_variant		5		ENSP00000359517.1
KYAT3	ENST00000446900.6	n.703-63C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47685 AN: 151712 Hom.: 8312 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.374 AC: 462238 AN: 1236216 Hom.: 88304 AF XY: 0.371 AC XY: 228004 AN XY: 614746

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.426

Gnomad4 ASJ exome AF: 0.312

Gnomad4 EAS exome AF: 0.399

Gnomad4 SAS exome AF: 0.254

Gnomad4 FIN exome AF: 0.315

Gnomad4 NFE exome AF: 0.392

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.314 AC: 47742 AN: 151832 Hom.: 8326 Cov.: 32 AF XY: 0.309 AC XY: 22946 AN XY: 74170

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.335

Alfa AF: 0.363 Hom.: 4851

Bravo AF: 0.322

Asia WGS AF: 0.307 AC: 1066 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.60

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: rs10922530; hg19: chr1-89427252; COSMIC: COSV53106852;