1-88961888-G-C

Position:

• chr1-88961888-G-C

Variant summary

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

The NM_001008661.3(KYAT3):​c.540+171C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,072 control chromosomes in the GnomAD database, including 14,283 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 0.42 (14283 hom., cov: 32)
• Consequence: KYAT3 NM_001008661.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KYAT3	NM_001008661.3	c.540+171C>G		intron_variant		ENST00000260508.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KYAT3	ENST00000260508.9	c.540+171C>G		intron_variant		1	NM_001008661.3	A1
KYAT3	ENST00000370486.1	c.540+171C>G		intron_variant		5
KYAT3	ENST00000370491.7	c.438+171C>G		intron_variant		2		P4
KYAT3	ENST00000446900.6	n.702+171C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63885 AN: 151954 Hom.: 14258 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.421 AC: 63957 AN: 152072 Hom.: 14283 Cov.: 32 AF XY: 0.416 AC XY: 30919 AN XY: 74360

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.437

Alfa AF: 0.330 Hom.: 925

Bravo AF: 0.423

Asia WGS AF: 0.435 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.59

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: rs3753683; hg19: chr1-89427571;