Variant rs157584 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001128917.2(TOMM40):c.436-138T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 652,948 control chromosomes in the GnomAD database, including 87,339 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 0.58 ( 27574 hom., cov: 32)

Exomes 𝑓: 0.48 ( 59765 hom. )

Consequence

TOMM40
NM_001128917.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11

Variant links:

Genes affected

TOMM40 (HGNC:18001): (translocase of outer mitochondrial membrane 40) The protein encoded by this gene is localized in the outer membrane of the mitochondria. It is the channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex that is essential for import of protein precursors into mitochondria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

TOMM40 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TOMM40	NM_001128917.2 linkuse as main transcript	c.436-138T>C		intron_variant		ENST00000426677.7	NP_001122389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TOMM40	ENST00000426677.7 linkuse as main transcript	c.436-138T>C		intron_variant		1	NM_001128917.2	ENSP00000410339	P1	O96008-1

Frequencies

GnomAD3 genomes

AF:

0.582

AC:

88407

AN:

151966

Hom.:

27534

Cov.:

show subpopulations

Gnomad AFR

AF:

0.821

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.571

Gnomad ASJ

AF:

0.508

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.536

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.575

GnomAD4 exome

AF:

0.480

AC:

240297

AN:

500864

Hom.:

59765

AF XY:

0.476

AC XY:

123908

AN XY:

260212

show subpopulations

Gnomad4 AFR exome

AF:

0.825

Gnomad4 AMR exome

AF:

0.584

Gnomad4 ASJ exome

AF:

0.517

Gnomad4 EAS exome

AF:

0.311

Gnomad4 SAS exome

AF:

0.423

Gnomad4 FIN exome

AF:

0.524

Gnomad4 NFE exome

AF:

0.476

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.582

AC:

88508

AN:

152084

Hom.:

27574

Cov.:

AF XY:

0.581

AC XY:

43222

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.821

Gnomad4 AMR

AF:

0.570

Gnomad4 ASJ

AF:

0.508

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.432

Gnomad4 FIN

AF:

0.536

Gnomad4 NFE

AF:

0.481

Gnomad4 OTH

AF:

0.573

Alfa

AF:

0.569

Hom.:

5115

Bravo

AF:

0.596

Asia WGS

AF:

0.423

AC:

1474

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.7

DANN

Benign

0.43

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over