Genetic Variant KYAT1:c.-6-231T>C (chr9-128845642-A-G) – 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.-6-231T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 536,428 control chromosomes in the GnomAD database, including 118,930 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 0.55 ( 27948 hom., cov: 33)

Exomes 𝑓: 0.68 ( 90982 hom. )

Consequence

KYAT1
NM_004059.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.895

Publications

16 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:

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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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004059.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KYAT1	NM_004059.5	MANE Select	c.-6-231T>C	intron	N/A	NP_004050.3
KYAT1	NM_001352993.2		c.-44T>C	5_prime_UTR_premature_start_codon_gain	Exon 1 of 13	NP_001339922.1
KYAT1	NM_001352993.2		c.-44T>C	5_prime_UTR	Exon 1 of 13	NP_001339922.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KYAT1	ENST00000302586.8	TSL:1 MANE Select	c.-6-231T>C	intron	N/A	ENSP00000302227.3
KYAT1	ENST00000651925.1		c.274-231T>C	intron	N/A	ENSP00000498386.1
KYAT1	ENST00000462722.5	TSL:1	n.141-231T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.553

AC:

83996

AN:

151890

Hom.:

27942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.786

Gnomad AMR

AF:

0.692

Gnomad ASJ

AF:

0.676

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.774

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.588

GnomAD4 exome

AF:

0.679

AC:

261144

AN:

384420

Hom.:

90982

AF XY:

0.674

AC XY:

137684

AN XY:

204160

show subpopulations

African (AFR)

AF:

0.160

AC:

1574

AN:

9826

American (AMR)

AF:

0.732

AC:

11354

AN:

15512

Ashkenazi Jewish (ASJ)

AF:

0.683

AC:

7950

AN:

11636

East Asian (EAS)

AF:

0.622

AC:

15236

AN:

24494

South Asian (SAS)

AF:

0.574

AC:

25145

AN:

43808

European-Finnish (FIN)

AF:

0.785

AC:

19175

AN:

24438

Middle Eastern (MID)

AF:

0.622

AC:

1037

AN:

1668

European-Non Finnish (NFE)

AF:

0.715

AC:

165305

AN:

231110

Other (OTH)

AF:

0.655

AC:

14368

AN:

21928

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

3743

7486

11229

14972

18715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.553

AC:

84000

AN:

152008

Hom.:

27948

Cov.:

AF XY:

0.557

AC XY:

41441

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.156

AC:

6471

AN:

41420

American (AMR)

AF:

0.692

AC:

10575

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.676

AC:

2346

AN:

3470

East Asian (EAS)

AF:

0.622

AC:

3198

AN:

5140

South Asian (SAS)

AF:

0.554

AC:

2665

AN:

4812

European-Finnish (FIN)

AF:

0.774

AC:

8204

AN:

10604

Middle Eastern (MID)

AF:

0.534

AC:

156

AN:

292

European-Non Finnish (NFE)

AF:

0.712

AC:

48429

AN:

67976

Other (OTH)

AF:

0.587

AC:

1239

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1488

2976

4463

5951

7439

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.667

Hom.:

29801

Bravo

AF:

0.533

Asia WGS

AF:

0.561

AC:

1952

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.7

(source)

DANN

Benign

0.72

PhyloP100

-0.90

PromoterAI

0.14

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over