7-49983410-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_007009.3(ZPBP):c.893G>C(p.Trp298Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,613,196 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic 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 Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZPBP | ENST00000046087.7 | c.893G>C | p.Trp298Ser | missense_variant | Exon 7 of 8 | 1 | NM_007009.3 | ENSP00000046087.2 | ||
ZPBP | ENST00000419417.5 | c.890G>C | p.Trp297Ser | missense_variant | Exon 7 of 8 | 1 | ENSP00000402071.1 | |||
ZPBP | ENST00000491129.5 | n.350G>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151918Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251250Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135808
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461278Hom.: 2 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 726954
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151918Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74214
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.893G>C (p.W298S) alteration is located in exon 7 (coding exon 7) of the ZPBP gene. This alteration results from a G to C substitution at nucleotide position 893, causing the tryptophan (W) at amino acid position 298 to be replaced by a serine (S). 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