NM_001128917.2:c.274+320G>A

Variant names:

• chr19-44892009-G-A
• rs157580
• NM_001128917.2:c.274+320G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128917.2(TOMM40):​c.274+320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,936 control chromosomes in the GnomAD database, including 36,886 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 0.69 (36886 hom., cov: 31)
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 195 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128917.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOMM40	NM_001128917.2	MANE Select	c.274+320G>A		intron	N/A	NP_001122389.1
	TOMM40	NM_001128916.2		c.274+320G>A		intron	N/A	NP_001122388.1
	TOMM40	NM_006114.3		c.274+320G>A		intron	N/A	NP_006105.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOMM40	ENST00000426677.7	TSL:1 MANE Select	c.274+320G>A		intron	N/A	ENSP00000410339.1
	TOMM40	ENST00000252487.9	TSL:1	c.274+320G>A		intron	N/A	ENSP00000252487.4
	TOMM40	ENST00000405636.6	TSL:1	c.274+320G>A		intron	N/A	ENSP00000385184.2

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104279 AN: 151818 Hom.: 36820 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.653

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.687 AC: 104414 AN: 151936 Hom.: 36886 Cov.: 31 AF XY: 0.692 AC XY: 51363 AN XY: 74276

African (AFR) AF: 0.853 AC: 35335 AN: 41410

American (AMR) AF: 0.674 AC: 10296 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2355 AN: 5154

South Asian (SAS) AF: 0.538 AC: 2587 AN: 4812

European-Finnish (FIN) AF: 0.732 AC: 7721 AN: 10550

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41794 AN: 67958

Other (OTH) AF: 0.656 AC: 1381 AN: 2106

Alfa AF: 0.633 Hom.: 134728

Bravo AF: 0.689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.83
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs157580; hg19: chr19-45395266;