dbSNP rs10922530: KYAT3:c.541-63C>T (chr1-88961569-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001008661.3(KYAT3):c.541-63C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 1,388,048 control chromosomes in the GnomAD database, including 96,630 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 0.31 ( 8326 hom., cov: 32)

Exomes 𝑓: 0.37 ( 88304 hom. )

Consequence

KYAT3
NM_001008661.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.242

Publications

16 publications found

Variant links:

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]

KYAT3 links:

ENSG00000307240 (HGNC:):

ENSG00000307240 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KYAT3	NM_001008661.3 link	c.541-63C>T		intron_variant	Intron 6 of 13	ENST00000260508.9	NP_001008661.1	Q6YP21-1B4DW13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KYAT3	ENST00000260508.9 link	c.541-63C>T		intron_variant	Intron 6 of 13	1	NM_001008661.3	ENSP00000260508.4		Q6YP21-1

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47685

AN:

151712

Hom.:

8312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.334

GnomAD4 exome

AF:

0.374

AC:

462238

AN:

1236216

Hom.:

88304

AF XY:

0.371

AC XY:

228004

AN XY:

614746

show subpopulations

African (AFR)

AF:

0.163

AC:

4451

AN:

27372

American (AMR)

AF:

0.426

AC:

12684

AN:

29776

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

6543

AN:

20952

East Asian (EAS)

AF:

0.399

AC:

14906

AN:

37356

South Asian (SAS)

AF:

0.254

AC:

16520

AN:

64956

European-Finnish (FIN)

AF:

0.315

AC:

15313

AN:

48646

Middle Eastern (MID)

AF:

0.212

AC:

867

AN:

4086

European-Non Finnish (NFE)

AF:

0.392

AC:

372858

AN:

951316

Other (OTH)

AF:

0.350

AC:

18096

AN:

51756

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

13531

27062

40593

54124

67655

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11528

23056

34584

46112

57640

<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:

0.314

AC:

47742

AN:

151832

Hom.:

8326

Cov.:

AF XY:

0.309

AC XY:

22946

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.165

AC:

6828

AN:

41388

American (AMR)

AF:

0.409

AC:

6246

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3468

East Asian (EAS)

AF:

0.342

AC:

1771

AN:

5172

South Asian (SAS)

AF:

0.254

AC:

1218

AN:

4800

European-Finnish (FIN)

AF:

0.307

AC:

3223

AN:

10514

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.385

AC:

26120

AN:

67918

Other (OTH)

AF:

0.335

AC:

704

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1609

3219

4828

6438

8047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.363

Hom.:

5430

Bravo

AF:

0.322

Asia WGS

AF:

0.307

AC:

1066

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.2

(source)

DANN

Benign

0.60

PhyloP100

0.24

Mutation Taster

=100/0

polymorphism (auto)

(source)

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