19-44899791-CTTTTTTTTTTTTTTTTTTTTTTT-CTTTT

Position:

• chr19-44899791-CTTTTTTTTTTTTTTTTTTTTTTT-CTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001128917.2(TOMM40):​c.644-922_644-904delTTTTTTTTTTTTTTTTTTT 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 0.57 (11836 hom., cov: 0)
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TOMM40	NM_001128917.2	c.644-922_644-904delTTTTTTTTTTTTTTTTTTT		intron_variant		ENST00000426677.7	NP_001122389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TOMM40	ENST00000426677.7	c.644-922_644-904delTTTTTTTTTTTTTTTTTTT		intron_variant		1	NM_001128917.2	ENSP00000410339.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 52761 AN: 93264 Hom.: 11838 Cov.: 0

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.566 AC: 52755 AN: 93268 Hom.: 11836 Cov.: 0 AF XY: 0.573 AC XY: 24521 AN XY: 42818

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.589

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;