Genetic Variant KYAT1:c.439-19A>G (chr9-128837832-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004059.5(KYAT1):c.439-19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 1,612,462 control chromosomes in the GnomAD database, including 429,631 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 0.64 ( 33704 hom., cov: 31)

Exomes 𝑓: 0.73 ( 395927 hom. )

Consequence

KYAT1
NM_004059.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486

Publications

12 publications found

Variant links:

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 links:

KYAT1 (HGNC:):

KYAT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT1	NM_004059.5 link	c.439-19A>G		intron_variant	Intron 5 of 12	ENST00000302586.8	NP_004050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KYAT1	ENST00000302586.8 link	c.439-19A>G		intron_variant	Intron 5 of 12	1	NM_004059.5	ENSP00000302227.3
KYAT1	ENST00000651925.1 link	c.718-19A>G		intron_variant	Intron 7 of 28			ENSP00000498386.1

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

97159

AN:

151894

Hom.:

33697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.346

Gnomad AMI

AF:

0.794

Gnomad AMR

AF:

0.755

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.616

Gnomad FIN

AF:

0.828

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.749

Gnomad OTH

AF:

0.661

GnomAD2 exomes

AF:

0.720

AC:

179109

AN:

248868

AF XY:

0.719

show subpopulations

Gnomad AFR exome

AF:

0.336

Gnomad AMR exome

AF:

0.801

Gnomad ASJ exome

AF:

0.757

Gnomad EAS exome

AF:

0.727

Gnomad FIN exome

AF:

0.829

Gnomad NFE exome

AF:

0.748

Gnomad OTH exome

AF:

0.731

GnomAD4 exome

AF:

0.733

AC:

1069991

AN:

1460450

Hom.:

395927

Cov.:

AF XY:

0.731

AC XY:

531029

AN XY:

726586

show subpopulations

African (AFR)

AF:

0.331

AC:

11072

AN:

33454

American (AMR)

AF:

0.796

AC:

35598

AN:

44706

Ashkenazi Jewish (ASJ)

AF:

0.763

AC:

19911

AN:

26110

East Asian (EAS)

AF:

0.752

AC:

29838

AN:

39684

South Asian (SAS)

AF:

0.625

AC:

53896

AN:

86218

European-Finnish (FIN)

AF:

0.831

AC:

44324

AN:

53332

Middle Eastern (MID)

AF:

0.695

AC:

4003

AN:

5758

European-Non Finnish (NFE)

AF:

0.746

AC:

828658

AN:

1110846

Other (OTH)

AF:

0.707

AC:

42691

AN:

60342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

13740

27480

41221

54961

68701

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20122

40244

60366

80488

100610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.639

AC:

97203

AN:

152012

Hom.:

33704

Cov.:

AF XY:

0.645

AC XY:

47897

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.346

AC:

14362

AN:

41456

American (AMR)

AF:

0.756

AC:

11536

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.768

AC:

2664

AN:

3468

East Asian (EAS)

AF:

0.724

AC:

3730

AN:

5152

South Asian (SAS)

AF:

0.615

AC:

2959

AN:

4812

European-Finnish (FIN)

AF:

0.828

AC:

8762

AN:

10584

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.749

AC:

50886

AN:

67960

Other (OTH)

AF:

0.661

AC:

1396

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1538

3076

4614

6152

7690

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

770

1540

2310

3080

3850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.681

Hom.:

8689

Bravo

AF:

0.624

Asia WGS

AF:

0.656

AC:

2283

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.54

(source)

DANN

Benign

0.46

PhyloP100

-0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over