Variant rs201396618 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_000274.4(OAT):c.199+11_199+16dupAATTAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00286 in 1,610,558 control chromosomes in the GnomAD database, including 92 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0046 ( 15 hom., cov: 33)

Exomes 𝑓: 0.0027 ( 77 hom. )

Consequence

OAT
NM_000274.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.841

Variant links:

Genes affected

OAT (HGNC:8091): (ornithine aminotransferase) This gene encodes the mitochondrial enzyme ornithine aminotransferase, which is a key enzyme in the pathway that converts arginine and ornithine into the major excitatory and inhibitory neurotransmitters glutamate and GABA. Mutations that result in a deficiency of this enzyme cause the autosomal recessive eye disease Gyrate Atrophy. Alternatively spliced transcript variants encoding different isoforms have been described. Related pseudogenes have been defined on the X chromosome. [provided by RefSeq, Jan 2010]

OAT links:

OAT (HGNC:):

OAT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 10-124411956-A-ATTAATT is Benign according to our data. Variant chr10-124411956-A-ATTAATT is described in ClinVar as [Likely_benign]. Clinvar id is 556600.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00457 (696/152316) while in subpopulation EAS AF= 0.0179 (93/5194). AF 95% confidence interval is 0.015. There are 15 homozygotes in gnomad4. There are 524 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OAT	NM_000274.4 linkuse as main transcript	c.199+11_199+16dupAATTAA		intron_variant		ENST00000368845.6	NP_000265.1	P04181-1A0A140VJQ4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OAT	ENST00000368845.6 linkuse as main transcript	c.199+11_199+16dupAATTAA		intron_variant		1	NM_000274.4	ENSP00000357838.5		P04181-1

Frequencies

GnomAD3 genomes

AF:

0.00457

AC:

696

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0179

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.0507

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000779

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00683

AC:

1717

AN:

251420

Hom.:

AF XY:

0.00695

AC XY:

945

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.0000289

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.0263

Gnomad SAS exome

AF:

0.000392

Gnomad FIN exome

AF:

0.0494

Gnomad NFE exome

AF:

0.00102

Gnomad OTH exome

AF:

0.00537

GnomAD4 exome

AF:

0.00268

AC:

3903

AN:

1458242

Hom.:

Cov.:

AF XY:

0.00269

AC XY:

1949

AN XY:

725722

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.0258

Gnomad4 SAS exome

AF:

0.000603

Gnomad4 FIN exome

AF:

0.0446

Gnomad4 NFE exome

AF:

0.000237

Gnomad4 OTH exome

AF:

0.00285

GnomAD4 genome

AF:

0.00457

AC:

696

AN:

152316

Hom.:

Cov.:

AF XY:

0.00704

AC XY:

524

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0179

Gnomad4 SAS

AF:

0.000828

Gnomad4 FIN

AF:

0.0507

Gnomad4 NFE

AF:

0.000779

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00185

Hom.:

Asia WGS

AF:

0.00779

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Ornithine aminotransferase deficiency

Benign:2

Benign, criteria provided, single submitter	clinical testing	Counsyl	Feb 08, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 23, 2019

See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over