3-142848433-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013363.4(PCOLCE2):c.232A>G(p.Ile78Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 1,452,484 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_013363.4 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 |
---|---|---|---|---|---|---|---|
PCOLCE2 | NM_013363.4 | c.232A>G | p.Ile78Val | missense_variant | 3/9 | ENST00000295992.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCOLCE2 | ENST00000295992.8 | c.232A>G | p.Ile78Val | missense_variant | 3/9 | 1 | NM_013363.4 | P1 | |
PCOLCE2 | ENST00000648195.1 | c.232A>G | p.Ile78Val | missense_variant | 3/9 | ||||
PCOLCE2 | ENST00000485766.1 | c.232A>G | p.Ile78Val | missense_variant | 3/7 | 5 | |||
PCOLCE2 | ENST00000495732.5 | n.397A>G | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249532Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134858
GnomAD4 exome AF: 0.00000482 AC: 7AN: 1452484Hom.: 0 Cov.: 31 AF XY: 0.00000971 AC XY: 7AN XY: 720604
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.232A>G (p.I78V) alteration is located in exon 3 (coding exon 3) of the PCOLCE2 gene. This alteration results from a A to G substitution at nucleotide position 232, causing the isoleucine (I) at amino acid position 78 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