ENST00000569730.1:n.240+3019A>G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000569730.1(ENSG00000260413):n.240+3019A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 152,060 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
ENST00000569730.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX29P2 | NR_002939.3 | n.342+3019A>G | intron_variant | Intron 2 of 8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000260413 | ENST00000569730.1 | n.240+3019A>G | intron_variant | Intron 1 of 4 | 6 | |||||
ENSG00000198106 | ENST00000604430.1 | n.999+3019A>G | intron_variant | Intron 3 of 10 | 5 | |||||
ENSG00000284685 | ENST00000641956.1 | n.1006+3019A>G | intron_variant | Intron 4 of 7 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152060Hom.: 0 Cov.: 32
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at