2-10777652-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039362.2(ATP6V1C2):c.893C>T(p.Pro298Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039362.2 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 |
---|---|---|---|---|---|---|---|
ATP6V1C2 | NM_001039362.2 | c.893C>T | p.Pro298Leu | missense_variant | 11/14 | ENST00000272238.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V1C2 | ENST00000272238.9 | c.893C>T | p.Pro298Leu | missense_variant | 11/14 | 5 | NM_001039362.2 | ||
ATP6V1C2 | ENST00000635370.1 | c.923C>T | p.Pro308Leu | missense_variant | 11/14 | 5 | |||
ATP6V1C2 | ENST00000648362.1 | c.893C>T | p.Pro298Leu | missense_variant | 11/12 | ||||
ATP6V1C2 | ENST00000381661.3 | c.826-920C>T | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249472Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135362
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727204
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.893C>T (p.P298L) alteration is located in exon 11 (coding exon 10) of the ATP6V1C2 gene. This alteration results from a C to T substitution at nucleotide position 893, causing the proline (P) at amino acid position 298 to be replaced by a leucine (L). 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