dbSNP rs17523127: TOMM20:c.-339G>T (chr1-235129054-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014765.3(TOMM20):c.-339G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000663 in 150,904 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000066 ( 0 hom. )

Consequence

TOMM20
NM_014765.3 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.01

Publications

0 publications found

Variant links:

Genes affected

TOMM20 (HGNC:20947): (translocase of outer mitochondrial membrane 20) Enables protein-transporting ATPase activity and unfolded protein binding activity. Involved in protein targeting to mitochondrion. Located in mitochondria-associated endoplasmic reticulum membrane and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

TOMM20 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOMM20	NM_014765.3 link	c.-339G>T		upstream_gene_variant		ENST00000366607.5	NP_055580.1	Q15388A0A024R3W2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOMM20	ENST00000366607.5 link	c.-339G>T		upstream_gene_variant		1	NM_014765.3	ENSP00000355566.4		Q15388

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000663

AC:

AN:

150904

Hom.:

AF XY:

0.0000124

AC XY:

AN XY:

80512

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

4006

American (AMR)

AF:

0.00

AC:

AN:

5572

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4176

East Asian (EAS)

AF:

0.00

AC:

AN:

6904

South Asian (SAS)

AF:

0.0000442

AC:

AN:

22630

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7996

Middle Eastern (MID)

AF:

0.00

AC:

AN:

678

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

90384

Other (OTH)

AF:

0.00

AC:

AN:

8558

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.49

(source)

DANN

Benign

0.53

PhyloP100

-3.0

PromoterAI

-0.0080

Neutral

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over