rs61732273
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017866.6(TMEM70):āc.346C>Gā(p.Leu116Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 1,613,674 control chromosomes in the GnomAD database, including 463 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_017866.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM70 | NM_017866.6 | c.346C>G | p.Leu116Val | missense_variant | 3/3 | ENST00000312184.6 | |
TMEM70 | NM_001040613.3 | c.*36C>G | 3_prime_UTR_variant | 3/3 | |||
TMEM70 | NR_033334.2 | n.526C>G | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM70 | ENST00000312184.6 | c.346C>G | p.Leu116Val | missense_variant | 3/3 | 1 | NM_017866.6 | P1 | |
TMEM70 | ENST00000517439.1 | c.*36C>G | 3_prime_UTR_variant | 3/3 | 2 | ||||
TMEM70 | ENST00000519551.1 | n.237C>G | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
TMEM70 | ENST00000416961.6 | c.*103C>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0210 AC: 3189AN: 152128Hom.: 38 Cov.: 33
GnomAD3 exomes AF: 0.0235 AC: 5905AN: 251328Hom.: 91 AF XY: 0.0243 AC XY: 3296AN XY: 135856
GnomAD4 exome AF: 0.0202 AC: 29544AN: 1461428Hom.: 425 Cov.: 33 AF XY: 0.0209 AC XY: 15179AN XY: 727028
GnomAD4 genome ? AF: 0.0210 AC: 3200AN: 152246Hom.: 38 Cov.: 33 AF XY: 0.0225 AC XY: 1678AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2012 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Mitochondrial complex V (ATP synthase) deficiency nuclear type 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 25, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | TMEM70: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at