8-73976049-AGGCGGCAGGCG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.457
Variant links:
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]

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ACMG classification

Classification made for transcript

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
TMEM70ENST00000520167.5 linkuse as main transcriptn.317+163_317+173del intron_variant, non_coding_transcript_variant 2
TMEM70ENST00000523794.1 linkuse as main transcriptn.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
show subpopulations
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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJun 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71269968; hg19: chr8-74888284; API