NM_006093.4:c.664G>C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006093.4(PRG3):c.664G>C(p.Val222Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,542 control chromosomes in the GnomAD database, with no homozygous occurrence. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V222I) has been classified as Likely benign.
Frequency
Consequence
NM_006093.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152068Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250124Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135644
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460356Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726450
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 30 AF XY: 0.0000134 AC XY: 1AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.664G>C (p.V222L) alteration is located in exon 6 (coding exon 5) of the PRG3 gene. This alteration results from a G to C substitution at nucleotide position 664, causing the valine (V) at amino acid position 222 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