rs35401849
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001017392.5(SUGP2):c.1686G>A(p.Thr562=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001017392.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUGP2 | NM_001017392.5 | c.1686G>A | p.Thr562= | synonymous_variant | 3/11 | ENST00000452918.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUGP2 | ENST00000452918.7 | c.1686G>A | p.Thr562= | synonymous_variant | 3/11 | 1 | NM_001017392.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000578 AC: 88AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251124Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135760
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461852Hom.: 0 Cov.: 32 AF XY: 0.0000784 AC XY: 57AN XY: 727226
GnomAD4 genome ? AF: 0.000578 AC: 88AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at