chr8-73976049-AGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCG-A

Position:

• chr8-73976049-AGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000520167.5(TMEM70):​n.317+119_317+173del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 225,888 control chromosomes in the GnomAD database, including 32,608 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.33 (4754 hom., cov: 0)
  • Exomes 𝑓: 0.70 (27854 hom.)
• Consequence: TMEM70 ENST00000520167.5 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.351

Genes affected

TMEM70 (HGNC:26050): (transmembrane protein 70) This gene likely encodes a mitochondrial membrane protein. The encoded protein may play a role in biogenesis of mitochondrial ATP synthase. Mutations in this gene have been associated with neonatal mitochondrial encephalocardiomyopathy due to ATP synthase deficiency. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-73976049-AGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCG-A is Benign according to our data. Variant chr8-73976049-AGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCGGGCGGCAGGCG-A is described in ClinVar as [Benign]. Clinvar id is 1248803.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM70	ENST00000520167.5	n.317+119_317+173del		intron_variant, non_coding_transcript_variant		2
TMEM70	ENST00000523794.1	n.574+119_575-171del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.326 AC: 33615 AN: 103110 Hom.: 4740 Cov.: 0

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.696 AC: 85450 AN: 122690 Hom.: 27854 AF XY: 0.702 AC XY: 46091 AN XY: 65664

Gnomad4 AFR exome AF: 0.636

Gnomad4 AMR exome AF: 0.749

Gnomad4 ASJ exome AF: 0.693

Gnomad4 EAS exome AF: 0.557

Gnomad4 SAS exome AF: 0.862

Gnomad4 FIN exome AF: 0.649

Gnomad4 NFE exome AF: 0.675

Gnomad4 OTH exome AF: 0.675

GnomAD4 genome AF: 0.326 AC: 33668 AN: 103198 Hom.: 4754 Cov.: 0 AF XY: 0.329 AC XY: 16480 AN XY: 50124

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.348

Alfa AF: 0.0625 Hom.: 39

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

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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: rs71269968; hg19: chr8-74888284;