X-139774697-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001353812.2(ATP11C):c.2209T>G(p.Phe737Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000885 in 112,962 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353812.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP11C | NM_001353812.2 | c.2209T>G | p.Phe737Val | missense_variant | 19/30 | ENST00000682941.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP11C | ENST00000682941.1 | c.2209T>G | p.Phe737Val | missense_variant | 19/30 | NM_001353812.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000885 AC: 1AN: 112962Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35088
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1089742Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 356632
GnomAD4 genome ? AF: 0.00000885 AC: 1AN: 112962Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35088
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.2218T>G (p.F740V) alteration is located in exon 19 (coding exon 19) of the ATP11C gene. This alteration results from a T to G substitution at nucleotide position 2218, causing the phenylalanine (F) at amino acid position 740 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