dbSNP rs1056610: TOMM22:c.*232T>C (chr22-38684073-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_020243.5(TOMM22):c.*232T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 491,696 control chromosomes in the GnomAD database, including 30,753 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 0.37 ( 11145 hom., cov: 32)

Exomes 𝑓: 0.33 ( 19608 hom. )

Consequence

TOMM22
NM_020243.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.643

Publications

32 publications found

Variant links:

Genes affected

TOMM22 (HGNC:18002): (translocase of outer mitochondrial membrane 22) The protein encoded by this gene is an integral membrane protein of the mitochondrial outer membrane. The encoded protein interacts with TOMM20 and TOMM40, and forms a complex with several other proteins to import cytosolic preproteins into the mitochondrion. [provided by RefSeq, Jul 2008]

TOMM22 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOMM22	NM_020243.5 link	c.*232T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000216034.6	NP_064628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOMM22	ENST00000216034.6 link	c.*232T>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_020243.5	ENSP00000216034.4
TOMM22	ENST00000492561.1 link	n.695T>C		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56426

AN:

151970

Hom.:

11130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.506

Gnomad AMI

AF:

0.406

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.338

GnomAD4 exome

AF:

0.331

AC:

112351

AN:

339606

Hom.:

19608

Cov.:

AF XY:

0.328

AC XY:

58042

AN XY:

176888

show subpopulations

African (AFR)

AF:

0.510

AC:

5719

AN:

11214

American (AMR)

AF:

0.253

AC:

4138

AN:

16386

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

3447

AN:

11072

East Asian (EAS)

AF:

0.490

AC:

14096

AN:

28794

South Asian (SAS)

AF:

0.295

AC:

7334

AN:

24890

European-Finnish (FIN)

AF:

0.337

AC:

7720

AN:

22932

Middle Eastern (MID)

AF:

0.342

AC:

517

AN:

1512

European-Non Finnish (NFE)

AF:

0.310

AC:

62794

AN:

202524

Other (OTH)

AF:

0.325

AC:

6586

AN:

20282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3445

6890

10334

13779

17224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.371

AC:

56488

AN:

152090

Hom.:

11145

Cov.:

AF XY:

0.369

AC XY:

27462

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.506

AC:

20988

AN:

41474

American (AMR)

AF:

0.266

AC:

4068

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

1078

AN:

3470

East Asian (EAS)

AF:

0.462

AC:

2389

AN:

5166

South Asian (SAS)

AF:

0.314

AC:

1515

AN:

4818

European-Finnish (FIN)

AF:

0.338

AC:

3577

AN:

10572

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.319

AC:

21673

AN:

67982

Other (OTH)

AF:

0.342

AC:

723

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1703

3407

5110

6814

8517

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.325

Hom.:

11118

Bravo

AF:

0.371

Asia WGS

AF:

0.389

AC:

1357

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.2

(source)

DANN

Benign

0.59

PhyloP100

-0.64

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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