Variant 1-58481183-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_145243.5(OMA1):c.1366-9T>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00482 in 781,124 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0036 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0051 ( 17 hom. )

Consequence

OMA1
NM_145243.5 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00003934

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.57

Variant links:

Genes affected

OMA1 (HGNC:29661): (OMA1 zinc metallopeptidase) Enables metalloendopeptidase activity. Involved in several processes, including HRI-mediated signaling; proteolysis; and regulation of mitochondrion organization. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

OMA1 links:

DAB1 (HGNC:2661): (DAB adaptor protein 1) The laminar organization of multiple neuronal types in the cerebral cortex is required for normal cognitive function. In mice, the disabled-1 gene plays a central role in brain development, directing the migration of cortical neurons past previously formed neurons to reach their proper layer. This gene is similar to disabled-1, and the protein encoded by this gene is thought to be a signal transducer that interacts with protein kinase pathways to regulate neuronal positioning in the developing brain. [provided by RefSeq, Jan 2017]

DAB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 1-58481183-A-C is Benign according to our data. Variant chr1-58481183-A-C is described in ClinVar as [Benign]. Clinvar id is 780003.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OMA1	NM_145243.5 linkuse as main transcript	c.1366-9T>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000371226.8	NP_660286.1
DAB1	NM_001379461.1 linkuse as main transcript	c.-505+24877T>G		intron_variant			NP_001366390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OMA1	ENST00000371226.8 linkuse as main transcript	c.1366-9T>G		splice_polypyrimidine_tract_variant, intron_variant		1	NM_145243.5	ENSP00000360270	P1	Q96E52-1

Frequencies

GnomAD3 genomes

AF:

0.00363

AC:

552

AN:

152108

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000524

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00937

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00566

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00502

AC:

938

AN:

186996

Hom.:

AF XY:

0.00489

AC XY:

506

AN XY:

103442

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.000220

Gnomad ASJ exome

AF:

0.00424

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000460

Gnomad FIN exome

AF:

0.0133

Gnomad NFE exome

AF:

0.00710

Gnomad OTH exome

AF:

0.00463

GnomAD4 exome

AF:

0.00511

AC:

3212

AN:

628898

Hom.:

Cov.:

AF XY:

0.00491

AC XY:

1654

AN XY:

336682

show subpopulations

Gnomad4 AFR exome

AF:

0.000952

Gnomad4 AMR exome

AF:

0.000340

Gnomad4 ASJ exome

AF:

0.00384

Gnomad4 EAS exome

AF:

0.0000304

Gnomad4 SAS exome

AF:

0.0000369

Gnomad4 FIN exome

AF:

0.0131

Gnomad4 NFE exome

AF:

0.00595

Gnomad4 OTH exome

AF:

0.00460

GnomAD4 genome

AF:

0.00363

AC:

552

AN:

152226

Hom.:

Cov.:

AF XY:

0.00348

AC XY:

259

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00937

Gnomad4 NFE

AF:

0.00566

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00526

Hom.:

Bravo

AF:

0.00292

Asia WGS

AF:

0.000872

AC:

AN:

3456

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000039

dbscSNV1_RF

Benign

0.15

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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