chr19-44899862-C-T

Variant names:

• chr19-44899862-C-T
• rs417357
• NM_001128917.2:c.644-868C>T

Variant summary

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

The NM_001128917.2(TOMM40):​c.644-868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0332 in 133,552 control chromosomes in the GnomAD database, including 231 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 0.033 (231 hom., cov: 27)
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 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 = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOMM40	NM_001128917.2	c.644-868C>T		intron_variant	Intron 5 of 8	ENST00000426677.7	NP_001122389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOMM40	ENST00000426677.7	c.644-868C>T		intron_variant	Intron 5 of 8	1	NM_001128917.2	ENSP00000410339.1

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 4423 AN: 133462 Hom.: 231 Cov.: 27

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0167

Gnomad ASJ AF: 0.000882

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.00178

Gnomad FIN AF: 0.000700

Gnomad MID AF: 0.0111

Gnomad NFE AF: 0.000556

Gnomad OTH AF: 0.0200

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

GnomAD4 genome AF: 0.0332 AC: 4433 AN: 133552 Hom.: 231 Cov.: 27 AF XY: 0.0334 AC XY: 2101 AN XY: 62934

African (AFR) AF: 0.113 AC: 4112 AN: 36496

American (AMR) AF: 0.0167 AC: 182 AN: 10892

Ashkenazi Jewish (ASJ) AF: 0.000882 AC: 3 AN: 3400

East Asian (EAS) AF: 0.0123 AC: 50 AN: 4066

South Asian (SAS) AF: 0.00178 AC: 7 AN: 3936

European-Finnish (FIN) AF: 0.000700 AC: 5 AN: 7140

Middle Eastern (MID) AF: 0.0118 AC: 2 AN: 170

European-Non Finnish (NFE) AF: 0.000556 AC: 36 AN: 64766

Other (OTH) AF: 0.0199 AC: 36 AN: 1812

Alfa AF: 0.0137 Hom.: 22

Bravo AF: 0.0363

Asia WGS AF: 0.0100 AC: 35 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
DANN	Benign	0.74
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs417357; hg19: chr19-45403119;