dbSNP rs2286498: TOMM7:c.152+115A>G (chr7-22817885-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_019059.5(TOMM7):c.152+115A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 989,414 control chromosomes in the GnomAD database, including 93,122 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 0.48 ( 19431 hom., cov: 32)

Exomes 𝑓: 0.40 ( 73691 hom. )

Consequence

TOMM7
NM_019059.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

21 publications found

Variant links:

Genes affected

TOMM7 (HGNC:21648): (translocase of outer mitochondrial membrane 7) This gene encodes a subunit of the translocase of the outer mitochondrial membrane. The encoded protein regulates the assembly and stability of the translocase complex. [provided by RefSeq, Oct 2012]

TOMM7 Gene-Disease associations (from GenCC):

Garg-Mishra progeroid syndrome
Inheritance: AR Classification: MODERATE, LIMITED Submitted by: Ambry Genetics

TOMM7 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 (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019059.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TOMM7	NM_019059.5	MANE Select	c.152+115A>G	intron	N/A	NP_061932.1	Q9P0U1
TOMM7	NR_168014.1		n.178+115A>G	intron	N/A
TOMM7	NR_168015.1		n.130-4700A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TOMM7	ENST00000358435.9	TSL:1 MANE Select	c.152+115A>G	intron	N/A	ENSP00000351214.4	Q9P0U1
TOMM7	ENST00000496129.1	TSL:1	n.298A>G	non_coding_transcript_exon	Exon 2 of 2
TOMM7	ENST00000483581.1	TSL:1	n.336+115A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73045

AN:

151868

Hom.:

19402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.686

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.819

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.433

GnomAD4 exome

AF:

0.401

AC:

335908

AN:

837424

Hom.:

73691

Cov.:

AF XY:

0.403

AC XY:

174144

AN XY:

432538

show subpopulations

African (AFR)

AF:

0.691

AC:

14176

AN:

20518

American (AMR)

AF:

0.493

AC:

16674

AN:

33820

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

5957

AN:

19598

East Asian (EAS)

AF:

0.823

AC:

28674

AN:

34844

South Asian (SAS)

AF:

0.512

AC:

32401

AN:

63288

European-Finnish (FIN)

AF:

0.419

AC:

20675

AN:

49402

Middle Eastern (MID)

AF:

0.340

AC:

1222

AN:

3590

European-Non Finnish (NFE)

AF:

0.349

AC:

200189

AN:

573562

Other (OTH)

AF:

0.411

AC:

15940

AN:

38802

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

8817

17634

26450

35267

44084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4876

9752

14628

19504

24380

<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:

0.481

AC:

73135

AN:

151990

Hom.:

19431

Cov.:

AF XY:

0.484

AC XY:

36004

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.686

AC:

28428

AN:

41448

American (AMR)

AF:

0.452

AC:

6914

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

1055

AN:

3468

East Asian (EAS)

AF:

0.819

AC:

4240

AN:

5176

South Asian (SAS)

AF:

0.535

AC:

2577

AN:

4818

European-Finnish (FIN)

AF:

0.409

AC:

4315

AN:

10540

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.355

AC:

24132

AN:

67932

Other (OTH)

AF:

0.432

AC:

912

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1783

3566

5350

7133

8916

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.399

Hom.:

8785

Bravo

AF:

0.497

Asia WGS

AF:

0.649

AC:

2257

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.089

(source)

DANN

Benign

0.70

PhyloP100

-1.5

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over