rs61758740
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_138300.4(PYGO2):c.423G>A(p.Met141Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,456,446 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_138300.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYGO2 | NM_138300.4 | c.423G>A | p.Met141Ile | missense_variant | 3/3 | ENST00000368457.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYGO2 | ENST00000368457.3 | c.423G>A | p.Met141Ile | missense_variant | 3/3 | 1 | NM_138300.4 | P1 | |
PYGO2 | ENST00000368456.1 | c.312G>A | p.Met104Ile | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00273 AC: 414AN: 151768Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00142 AC: 209AN: 147278Hom.: 1 AF XY: 0.00108 AC XY: 85AN XY: 79060
GnomAD4 exome AF: 0.000850 AC: 1109AN: 1304560Hom.: 6 Cov.: 29 AF XY: 0.000809 AC XY: 515AN XY: 636288
GnomAD4 genome ? AF: 0.00271 AC: 412AN: 151886Hom.: 1 Cov.: 32 AF XY: 0.00261 AC XY: 194AN XY: 74214
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at