rs1962412
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_005175.3(ATP5MC1):c.-23T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 156,470 control chromosomes in the GnomAD database, including 33,187 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 0.64 ( 31906 hom., cov: 29)
Exomes 𝑓: 0.71 ( 1281 hom. )
Consequence
ATP5MC1
NM_005175.3 5_prime_UTR
NM_005175.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.918
Genes affected
ATP5MC1 (HGNC:841): (ATP synthase membrane subunit c locus 1) 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 seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene is one of three genes that encode subunit c of the proton channel. Each of the three genes have distinct mitochondrial import sequences but encode the identical mature protein. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP5MC1 | NM_005175.3 | c.-23T>C | 5_prime_UTR_variant | 1/5 | ENST00000393366.7 | ||
LOC105371814 | NR_135674.1 | n.46-220A>G | intron_variant, non_coding_transcript_variant | ||||
ATP5MC1 | NM_001002027.2 | c.-10+57T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP5MC1 | ENST00000393366.7 | c.-23T>C | 5_prime_UTR_variant | 1/5 | 1 | NM_005175.3 | P1 | ||
ENST00000508743.1 | n.46-220A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.642 AC: 97224AN: 151384Hom.: 31900 Cov.: 29
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GnomAD4 exome AF: 0.713 AC: 3540AN: 4968Hom.: 1281 Cov.: 0 AF XY: 0.711 AC XY: 2281AN XY: 3206
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GnomAD4 genome ? AF: 0.642 AC: 97261AN: 151502Hom.: 31906 Cov.: 29 AF XY: 0.642 AC XY: 47518AN XY: 73982
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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