rs964184
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003904(ZPR1):c.*724C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152052 control chromosomes in the gnomAD Genomes database, including 51754 homozygotes. 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
Genomes: 𝑓 0.82 ( 51754 hom., cov: 32)
Consequence
ZPR1
NM_003904 3_prime_UTR
NM_003904 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.346
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZPR1 | NM_003904.5 | c.*724C>G | 3_prime_UTR_variant | 14/14 | ENST00000227322.8 | ||
ZPR1 | NM_001317086.2 | c.*724C>G | 3_prime_UTR_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZPR1 | ENST00000227322.8 | c.*724C>G | 3_prime_UTR_variant | 14/14 | 1 | NM_003904.5 | P1 | ||
ZPR1 | ENST00000429220.5 | c.*724C>G | 3_prime_UTR_variant | 12/12 | 5 | ||||
ZPR1 | ENST00000444935.5 | c.*724C>G | 3_prime_UTR_variant | 13/13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.823 AC: 125152AN: 152052Hom.: 51754 Cov.: 32
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GnomAD4 exome AF: 0.882 AC: 60AN: 68Hom.: 26 AF XY: 0.909 AC XY: 40AN XY: 44
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at