chr10-7802423-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001001973.3(ATP5F1C):c.791C>T(p.Ala264Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,611,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001973.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP5F1C | NM_001001973.3 | c.791C>T | p.Ala264Val | missense_variant, splice_region_variant | 7/10 | ENST00000356708.12 | |
LOC105376392 | XR_001747356.1 | n.192-2922G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP5F1C | ENST00000356708.12 | c.791C>T | p.Ala264Val | missense_variant, splice_region_variant | 7/10 | 1 | NM_001001973.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247318Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133592
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1459138Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 725812
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.791C>T (p.A264V) alteration is located in exon 7 (coding exon 7) of the ATP5C1 gene. This alteration results from a C to T substitution at nucleotide position 791, causing the alanine (A) at amino acid position 264 to be replaced by a valine (V). 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