rs202177059
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013363.4(PCOLCE2):c.332G>A(p.Arg111Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000855 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251456Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135906
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 727248
GnomAD4 genome AF: 0.000125 AC: 19AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.332G>A (p.R111Q) alteration is located in exon 3 (coding exon 3) of the PCOLCE2 gene. This alteration results from a G to A substitution at nucleotide position 332, causing the arginine (R) at amino acid position 111 to be replaced by a glutamine (Q). 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