8-73976049-A-AGGCGGCAGGCGGGCGGCAGGCG

Position:

• chr8-73976049-A-AGGCGGCAGGCGGGCGGCAGGCG

Variant summary

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

The ENST00000520167.5(TMEM70):​n.317+152_317+173dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.084 (1444 hom., cov: 0)
  • Exomes 𝑓: 0.0000081 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TMEM70 ENST00000520167.5 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.111

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-A-AGGCGGCAGGCGGGCGGCAGGCG is Benign according to our data. Variant chr8-73976049-A-AGGCGGCAGGCGGGCGGCAGGCG is described in ClinVar as [Benign]. Clinvar id is 1234801.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 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+152_317+173dup		intron_variant, non_coding_transcript_variant		2
TMEM70	ENST00000523794.1	n.574+152_575-171dup		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 8710 AN: 103250 Hom.: 1441 Cov.: 0

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.0688

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0661

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0908

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000815 AC: 1 AN: 122740 Hom.: 0 Cov.: 0 AF XY: 0.0000152 AC XY: 1 AN XY: 65694

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000151

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0843 AC: 8714 AN: 103338 Hom.: 1444 Cov.: 0 AF XY: 0.0810 AC XY: 4063 AN XY: 50186

Gnomad4 AFR AF: 0.0640

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0573

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0899

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

Sep 09, 2019

- -

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;