ENST00000531894.5:n.562-981A>G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000531894.5(PDXDC2P-NPIPB14P):n.562-981A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 152,280 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
ENST00000531894.5 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 |
---|---|---|---|---|---|---|---|---|
PDXDC2P | n.70035341T>C | intragenic_variant | ||||||
PDXDC2P-NPIPB14P | NR_003610.1 | n.562-981A>G | intron_variant | Intron 5 of 25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDXDC2P-NPIPB14P | ENST00000531894.5 | n.562-981A>G | intron_variant | Intron 5 of 25 | 1 | |||||
PDXDC2P-NPIPB14P | ENST00000529089.1 | n.432-981A>G | intron_variant | Intron 5 of 17 | 2 | |||||
PDXDC2P-NPIPB14P | ENST00000530079.5 | n.582-981A>G | intron_variant | Intron 5 of 24 | 5 | |||||
PDXDC2P | ENST00000534700.6 | n.390-981A>G | intron_variant | Intron 5 of 15 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152162Hom.: 0 Cov.: 32
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74468
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at