rs2286498

Positions:

• chr7-22817885-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019059.5(TOMM7):​c.152+115A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 989,414 control chromosomes in the GnomAD database, including 93,122 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 0.48 (19431 hom., cov: 32)
  • Exomes 𝑓: 0.40 (73691 hom.)
• Consequence: TOMM7 NM_019059.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

TOMM7 (HGNC:21648): (translocase of outer mitochondrial membrane 7) This gene encodes a subunit of the translocase of the outer mitochondrial membrane. The encoded protein regulates the assembly and stability of the translocase complex. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TOMM7	NM_019059.5	c.152+115A>G		intron_variant		ENST00000358435.9
TOMM7	NR_168014.1	n.178+115A>G		intron_variant, non_coding_transcript_variant
TOMM7	NR_168015.1	n.130-4700A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TOMM7	ENST00000358435.9	c.152+115A>G		intron_variant		1	NM_019059.5	P1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73045 AN: 151868 Hom.: 19402 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.433

GnomAD4 exome AF: 0.401 AC: 335908 AN: 837424 Hom.: 73691 Cov.: 11 AF XY: 0.403 AC XY: 174144 AN XY: 432538

Gnomad4 AFR exome AF: 0.691

Gnomad4 AMR exome AF: 0.493

Gnomad4 ASJ exome AF: 0.304

Gnomad4 EAS exome AF: 0.823

Gnomad4 SAS exome AF: 0.512

Gnomad4 FIN exome AF: 0.419

Gnomad4 NFE exome AF: 0.349

Gnomad4 OTH exome AF: 0.411

GnomAD4 genome AF: 0.481 AC: 73135 AN: 151990 Hom.: 19431 Cov.: 32 AF XY: 0.484 AC XY: 36004 AN XY: 74316

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.432

Alfa AF: 0.401 Hom.: 6690

Bravo AF: 0.497

Asia WGS AF: 0.649 AC: 2257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.089
DANN	Benign	0.70

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

LitVar

Other links and lift over

dbSNP: rs2286498; hg19: chr7-22857504;