2-169630791-A-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004792.3(PPIG):c.565A>C(p.Lys189Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000501 in 1,596,072 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_004792.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPIG | NM_004792.3 | c.565A>C | p.Lys189Gln | missense_variant | Exon 10 of 14 | ENST00000260970.8 | NP_004783.2 | |
PPIG | XM_005246966.3 | c.565A>C | p.Lys189Gln | missense_variant | Exon 10 of 14 | XP_005247023.1 | ||
PPIG | XM_005246967.2 | c.565A>C | p.Lys189Gln | missense_variant | Exon 10 of 14 | XP_005247024.1 | ||
PPIG | XM_017005302.3 | c.565A>C | p.Lys189Gln | missense_variant | Exon 10 of 12 | XP_016860791.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000429 AC: 1AN: 233118Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126470
GnomAD4 exome AF: 0.00000485 AC: 7AN: 1443900Hom.: 0 Cov.: 31 AF XY: 0.00000418 AC XY: 3AN XY: 717794
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.565A>C (p.K189Q) alteration is located in exon 10 (coding exon 8) of the PPIG gene. This alteration results from a A to C substitution at nucleotide position 565, causing the lysine (K) at amino acid position 189 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