chr4-119030492-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000307142.9(SYNPO2):āc.1717A>Gā(p.Thr573Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 1,613,934 control chromosomes in the GnomAD database, including 596,283 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000307142.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNPO2 | NM_133477.3 | c.1717A>G | p.Thr573Ala | missense_variant | 4/5 | ENST00000307142.9 | NP_597734.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNPO2 | ENST00000307142.9 | c.1717A>G | p.Thr573Ala | missense_variant | 4/5 | 1 | NM_133477.3 | ENSP00000306015 | P1 |
Frequencies
GnomAD3 genomes AF: 0.852 AC: 129464AN: 151940Hom.: 55223 Cov.: 30
GnomAD3 exomes AF: 0.853 AC: 214250AN: 251162Hom.: 91656 AF XY: 0.851 AC XY: 115551AN XY: 135746
GnomAD4 exome AF: 0.860 AC: 1256920AN: 1461876Hom.: 541012 Cov.: 88 AF XY: 0.858 AC XY: 623903AN XY: 727232
GnomAD4 genome AF: 0.852 AC: 129573AN: 152058Hom.: 55271 Cov.: 30 AF XY: 0.850 AC XY: 63177AN XY: 74322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at