chr8-73976049-AGGCGGCAGGCG-A

Position:

• chr8-73976049-AGGCGGCAGGCG-A

Variant summary

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

The ENST00000520167.5(TMEM70):​n.317+163_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 0.0301 in 224,972 control chromosomes in the GnomAD database, including 255 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.058 (202 hom., cov: 0)
  • Exomes 𝑓: 0.0068 (53 hom.)
• Consequence: TMEM70 ENST00000520167.5 intron, non_coding_transcript
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.457

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-AGGCGGCAGGCG-A is Benign according to our data. Variant chr8-73976049-AGGCGGCAGGCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 1183909.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-73976049-AGGCGGCAGGCG-A is described in Lovd as [Benign]. Variant chr8-73976049-AGGCGGCAGGCG-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0688 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+163_317+173del		intron_variant, non_coding_transcript_variant		2
TMEM70	ENST00000523794.1	n.574+163_575-171del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 5934 AN: 103170 Hom.: 203 Cov.: 0

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0309

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0474

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0496

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0565

GnomAD4 exome AF: 0.00683 AC: 831 AN: 121718 Hom.: 53 AF XY: 0.00707 AC XY: 461 AN XY: 65194

Gnomad4 AFR exome AF: 0.00825

Gnomad4 AMR exome AF: 0.00345

Gnomad4 ASJ exome AF: 0.00452

Gnomad4 EAS exome AF: 0.00760

Gnomad4 SAS exome AF: 0.00302

Gnomad4 FIN exome AF: 0.0107

Gnomad4 NFE exome AF: 0.00774

Gnomad4 OTH exome AF: 0.00753

GnomAD4 genome AF: 0.0576 AC: 5944 AN: 103254 Hom.: 202 Cov.: 0 AF XY: 0.0570 AC XY: 2860 AN XY: 50134

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.0497

Gnomad4 ASJ AF: 0.0474

Gnomad4 EAS AF: 0.0769

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.0588

Gnomad4 OTH AF: 0.0573

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 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;