rs34896370

Variant names:

• chr19-44898511-CTT-C
• rs34896370
• NM_001128917.2:c.644-2207_644-2206delTT

Your query was ambiguous. Multiple possible variants found:

• chr19-44898511-CTT-C
• chr19-44898511-CTT-CT
• chr19-44898511-CTT-CTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTCTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTGTTTTTT
• chr19-44898511-CTT-CTTTT
• chr19-44898511-CTT-CTTTTT
• chr19-44898511-CTT-CTTTTTT
• chr19-44898511-CTT-CTTTTTTT
• chr19-44898511-CTT-CTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
• chr19-44898511-CTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001128917.2(TOMM40):​c.644-2207_644-2206delTT 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 0.000061 (0 hom., cov: 0)
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOMM40	NM_001128917.2	c.644-2207_644-2206delTT		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.644-2218_644-2217delTT		intron_variant	Intron 5 of 8	1	NM_001128917.2	ENSP00000410339.1

Frequencies

GnomAD3 genomes AF: 0.0000609 AC: 6 AN: 98536 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000832

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000764

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000609 AC: 6 AN: 98522 Hom.: 0 Cov.: 0 AF XY: 0.0000443 AC XY: 2 AN XY: 45106

African (AFR) AF: 0.0000832 AC: 2 AN: 24046

American (AMR) AF: 0.00 AC: 0 AN: 8556

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2796

East Asian (EAS) AF: 0.00 AC: 0 AN: 3520

South Asian (SAS) AF: 0.00 AC: 0 AN: 2826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2216

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 126

European-Non Finnish (NFE) AF: 0.0000764 AC: 4 AN: 52354

Other (OTH) AF: 0.00 AC: 0 AN: 1346

Alfa AF: 0.00 Hom.: 259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.41

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

Publications

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Other links and lift over

dbSNP: rs34896370; hg19: chr19-45401768;