19-44899791-CTTTTTTTTTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTT

Position:

• chr19-44899791-CTTTTTTTTTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001128917.2(TOMM40):​c.644-905_644-904dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0051 (48 hom., cov: 0)
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 460 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TOMM40	NM_001128917.2	c.644-905_644-904dup		intron_variant		ENST00000426677.7	NP_001122389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TOMM40	ENST00000426677.7	c.644-905_644-904dup		intron_variant		1	NM_001128917.2	ENSP00000410339	P1

Frequencies

GnomAD3 genomes AF: 0.00505 AC: 459 AN: 90854 Hom.: 48 Cov.: 0

Gnomad AFR AF: 0.00190

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.00443

Gnomad ASJ AF: 0.00584

Gnomad EAS AF: 0.00376

Gnomad SAS AF: 0.00276

Gnomad FIN AF: 0.000302

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00755

Gnomad OTH AF: 0.00327

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

GnomAD4 genome AF: 0.00506 AC: 460 AN: 90862 Hom.: 48 Cov.: 0 AF XY: 0.00461 AC XY: 192 AN XY: 41680

Gnomad4 AFR AF: 0.00189

Gnomad4 AMR AF: 0.00442

Gnomad4 ASJ AF: 0.00584

Gnomad4 EAS AF: 0.00377

Gnomad4 SAS AF: 0.00277

Gnomad4 FIN AF: 0.000302

Gnomad4 NFE AF: 0.00755

Gnomad4 OTH AF: 0.00324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10524523; hg19: chr19-45403048;