rs4655
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001001973.3(ATP5F1C):c.*97T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,557,388 control chromosomes in the GnomAD database, including 103,286 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 9230 hom., cov: 32)
Exomes 𝑓: 0.36 ( 94056 hom. )
Consequence
ATP5F1C
NM_001001973.3 3_prime_UTR
NM_001001973.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.21
Genes affected
ATP5F1C (HGNC:833): (ATP synthase F1 subunit gamma) This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the gamma subunit of the catalytic core. Alternatively spliced transcript variants encoding different isoforms have been identified. This gene also has a pseudogene on chromosome 14. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP5F1C | NM_001001973.3 | c.*97T>C | 3_prime_UTR_variant | 10/10 | ENST00000356708.12 | ||
LOC105376392 | XR_001747356.1 | n.191+739A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP5F1C | ENST00000356708.12 | c.*97T>C | 3_prime_UTR_variant | 10/10 | 1 | NM_001001973.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.348 AC: 52876AN: 151980Hom.: 9230 Cov.: 32
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GnomAD4 exome AF: 0.364 AC: 512211AN: 1405290Hom.: 94056 Cov.: 25 AF XY: 0.365 AC XY: 255610AN XY: 699756
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GnomAD4 genome ? AF: 0.348 AC: 52902AN: 152098Hom.: 9230 Cov.: 32 AF XY: 0.347 AC XY: 25832AN XY: 74358
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at