7-50093121-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007009.3(ZPBP):c.74G>A(p.Arg25Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,580,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R25P) has been classified as Benign.
Frequency
Consequence
NM_007009.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZPBP | NM_007009.3 | c.74G>A | p.Arg25Gln | missense_variant | 1/8 | ENST00000046087.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZPBP | ENST00000046087.7 | c.74G>A | p.Arg25Gln | missense_variant | 1/8 | 1 | NM_007009.3 | P4 | |
ZPBP | ENST00000419417.5 | c.74G>A | p.Arg25Gln | missense_variant | 1/8 | 1 | A2 | ||
ZPBP | ENST00000450231.1 | c.11-3412G>A | intron_variant | 3 | |||||
ZPBP | ENST00000413331.1 | c.74G>A | p.Arg25Gln | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000328 AC: 6AN: 183006Hom.: 0 AF XY: 0.0000300 AC XY: 3AN XY: 100112
GnomAD4 exome AF: 0.0000301 AC: 43AN: 1428196Hom.: 0 Cov.: 30 AF XY: 0.0000325 AC XY: 23AN XY: 707644
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74472
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at