10-7788251-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001001973.3(ATP5F1C):c.44T>C(p.Leu15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,152 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001001973.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP5F1C | NM_001001973.3 | c.44T>C | p.Leu15Ser | missense_variant | 1/10 | ENST00000356708.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP5F1C | ENST00000356708.12 | c.44T>C | p.Leu15Ser | missense_variant | 1/10 | 1 | NM_001001973.3 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248934Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134780
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461152Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726870
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | The c.44T>C (p.L15S) alteration is located in exon 1 (coding exon 1) of the ATP5C1 gene. This alteration results from a T to C substitution at nucleotide position 44, causing the leucine (L) at amino acid position 15 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at