7-49937527-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_007009.3(ZPBP):c.*1G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,610,108 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_007009.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZPBP | ENST00000046087 | c.*1G>A | 3_prime_UTR_variant | Exon 8 of 8 | 1 | NM_007009.3 | ENSP00000046087.2 | |||
ZPBP | ENST00000491129.5 | n.419-36312G>A | intron_variant | Intron 2 of 3 | 3 | |||||
ZPBP | ENST00000419417.5 | c.*1G>A | downstream_gene_variant | 1 | ENSP00000402071.1 |
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 229AN: 152052Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000283 AC: 71AN: 251256Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135784
GnomAD4 exome AF: 0.000115 AC: 167AN: 1457938Hom.: 0 Cov.: 29 AF XY: 0.0000923 AC XY: 67AN XY: 725536
GnomAD4 genome AF: 0.00154 AC: 234AN: 152170Hom.: 3 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74380
ClinVar
Submissions by phenotype
ZPBP-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at