Genetic Variant KYAT1:n.1903G>A (chr9-128833128-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000462722.5(KYAT1):n.1903G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 172,850 control chromosomes in the GnomAD database, including 11,108 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 0.34 ( 10555 hom., cov: 31)

Exomes 𝑓: 0.20 ( 553 hom. )

Consequence

KYAT1
ENST00000462722.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.72

Publications

22 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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT1	NM_004059.5 link	c.*456G>A		3_prime_UTR_variant	Exon 13 of 13	ENST00000302586.8	NP_004050.3	Q16773-1A8K563

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KYAT1	ENST00000302586.8 link	c.*456G>A		3_prime_UTR_variant	Exon 13 of 13	1	NM_004059.5	ENSP00000302227.3		Q16773-1
KYAT1	ENST00000651925.1 link	c.*357+99G>A		intron_variant	Intron 15 of 28			ENSP00000498386.1		A0A494C066

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51521

AN:

151720

Hom.:

10544

Cov.:

show subpopulations

Gnomad AFR

AF:

0.584

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.328

GnomAD4 exome

AF:

0.200

AC:

4198

AN:

21012

Hom.:

553

Cov.:

AF XY:

0.207

AC XY:

2209

AN XY:

10656

show subpopulations

African (AFR)

AF:

0.494

AC:

245

AN:

496

American (AMR)

AF:

0.178

AC:

360

AN:

2028

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

AN:

568

East Asian (EAS)

AF:

0.194

AC:

189

AN:

976

South Asian (SAS)

AF:

0.267

AC:

387

AN:

1450

European-Finnish (FIN)

AF:

0.121

AC:

AN:

654

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.189

AC:

2574

AN:

13590

Other (OTH)

AF:

0.212

AC:

250

AN:

1182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

145

290

434

579

724

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

192

240

<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:

0.340

AC:

51577

AN:

151838

Hom.:

10555

Cov.:

AF XY:

0.335

AC XY:

24842

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.583

AC:

24136

AN:

41382

American (AMR)

AF:

0.237

AC:

3606

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

822

AN:

3466

East Asian (EAS)

AF:

0.276

AC:

1419

AN:

5150

South Asian (SAS)

AF:

0.384

AC:

1837

AN:

4788

European-Finnish (FIN)

AF:

0.171

AC:

1810

AN:

10570

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

16957

AN:

67926

Other (OTH)

AF:

0.328

AC:

694

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1532

3064

4596

6128

7660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.279

Hom.:

10597

Bravo

AF:

0.352

Asia WGS

AF:

0.339

AC:

1180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

2.1

(source)

DANN

Benign

0.77

PhyloP100

-2.7

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

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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