rs200053998
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014224.5(PGA5):c.664A>C(p.Lys222Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 152,138 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014224.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGA5 | ENST00000312403.10 | c.664A>C | p.Lys222Gln | missense_variant | Exon 6 of 9 | 1 | NM_014224.5 | ENSP00000309542.6 | ||
PGA5 | ENST00000451616.6 | c.202A>C | p.Lys68Gln | missense_variant | Exon 1 of 4 | 2 | ENSP00000408739.2 | |||
ENSG00000256220 | ENST00000537594.1 | n.160A>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00421 AC: 640AN: 152020Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.00309 AC: 775AN: 251000Hom.: 10 AF XY: 0.00293 AC XY: 397AN XY: 135654
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00194 AC: 2823AN: 1456138Hom.: 31 Cov.: 31 AF XY: 0.00194 AC XY: 1409AN XY: 724632
GnomAD4 genome AF: 0.00421 AC: 641AN: 152138Hom.: 14 Cov.: 32 AF XY: 0.00389 AC XY: 289AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:1
PGA5: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at