chr7-50089694-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007009.3(ZPBP):c.143G>A(p.Arg48Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,610,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007009.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZPBP | NM_007009.3 | c.143G>A | p.Arg48Gln | missense_variant | 2/8 | ENST00000046087.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZPBP | ENST00000046087.7 | c.143G>A | p.Arg48Gln | missense_variant | 2/8 | 1 | NM_007009.3 | P4 | |
ZPBP | ENST00000419417.5 | c.143G>A | p.Arg48Gln | missense_variant | 2/8 | 1 | A2 | ||
ZPBP | ENST00000450231.1 | c.26G>A | p.Arg9Gln | missense_variant | 4/5 | 3 | |||
ZPBP | ENST00000413331.1 | c.*120G>A | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151948Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248720Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134464
GnomAD4 exome AF: 0.0000439 AC: 64AN: 1458362Hom.: 0 Cov.: 30 AF XY: 0.0000510 AC XY: 37AN XY: 725400
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151948Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74216
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.143G>A (p.R48Q) alteration is located in exon 2 (coding exon 2) of the ZPBP gene. This alteration results from a G to A substitution at nucleotide position 143, causing the arginine (R) at amino acid position 48 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at