8-73976049-AGGCGGCAGGCG-A
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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
ENST00000520167.5 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
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]
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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 |
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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: 5934AN: 103170Hom.: 203 Cov.: 0
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GnomAD4 exome AF: 0.00683 AC: 831AN: 121718Hom.: 53 AF XY: 0.00707 AC XY: 461AN XY: 65194
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GnomAD4 genome AF: 0.0576 AC: 5944AN: 103254Hom.: 202 Cov.: 0 AF XY: 0.0570 AC XY: 2860AN XY: 50134
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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 submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at