11-57389258-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002728.6(PRG2):c.118G>A(p.Glu40Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002728.6 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 |
---|---|---|---|---|---|---|---|
PRG2 | NM_002728.6 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 | ENST00000311862.10 | |
PRG2 | NM_001302926.2 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 | ||
PRG2 | NM_001302927.2 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 | ||
PRG2 | NM_001243245.3 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRG2 | ENST00000311862.10 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 | 1 | NM_002728.6 | P1 | |
PRG2 | ENST00000525955.1 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 | 2 | P1 | ||
PRG2 | ENST00000533605.5 | c.118G>A | p.Glu40Lys | missense_variant | 3/6 | 5 | |||
PRG2 | ENST00000530105.1 | n.164G>A | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461824Hom.: 1 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727214
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2021 | The c.118G>A (p.E40K) alteration is located in exon 3 (coding exon 2) of the PRG2 gene. This alteration results from a G to A substitution at nucleotide position 118, causing the glutamic acid (E) at amino acid position 40 to be replaced by a lysine (K). 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