chr1-88971430-G-T

Variant names:

• chr1-88971430-G-T
• rs10518418
• NM_001008661.3:c.100-1963C>A

Variant summary

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

The NM_001008661.3(KYAT3):​c.100-1963C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,644 control chromosomes in the GnomAD database, including 918 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 (918 hom., cov: 32)
• Consequence: KYAT3 NM_001008661.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT3	NM_001008661.3	c.100-1963C>A		intron_variant	Intron 2 of 13	ENST00000260508.9	NP_001008661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KYAT3	ENST00000260508.9	c.100-1963C>A		intron_variant	Intron 2 of 13	1	NM_001008661.3	ENSP00000260508.4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16089 AN: 151528 Hom.: 915 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.106 AC: 16106 AN: 151644 Hom.: 918 Cov.: 32 AF XY: 0.107 AC XY: 7889 AN XY: 74046

African (AFR) AF: 0.105 AC: 4343 AN: 41314

American (AMR) AF: 0.0754 AC: 1149 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3470

East Asian (EAS) AF: 0.115 AC: 595 AN: 5152

South Asian (SAS) AF: 0.0646 AC: 310 AN: 4798

European-Finnish (FIN) AF: 0.150 AC: 1570 AN: 10442

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7514 AN: 67920

Other (OTH) AF: 0.103 AC: 218 AN: 2110

Alfa AF: 0.107 Hom.: 607

Bravo AF: 0.100

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.65
PhyloP100		0.23
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: rs10518418; hg19: chr1-89437113;