rs764551
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_153688.4(ZFP1):c.*50C>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 0.127 in 1,507,764 control chromosomes in the GnomAD database, including 20,063 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 0.11 ( 1932 hom., cov: 32)
Exomes 𝑓: 0.13 ( 18131 hom. )
Consequence
ZFP1
NM_153688.4 3_prime_UTR
NM_153688.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.31
Genes affected
ZFP1 (HGNC:23328): (ZFP1 zinc finger protein) This gene belongs to the zinc finger protein family. Some members of this family bind to DNA by zinc-mediated secondary structures called zinc fingers, and are involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFP1 | NM_153688.4 | c.*50C>A | 3_prime_UTR_variant | 4/4 | ENST00000570010.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFP1 | ENST00000570010.6 | c.*50C>A | 3_prime_UTR_variant | 4/4 | 2 | NM_153688.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17327AN: 151986Hom.: 1931 Cov.: 32
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GnomAD3 exomes AF: 0.176 AC: 30606AN: 174116Hom.: 4685 AF XY: 0.175 AC XY: 16157AN XY: 92418
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GnomAD4 exome AF: 0.129 AC: 174443AN: 1355662Hom.: 18131 Cov.: 31 AF XY: 0.132 AC XY: 87373AN XY: 663196
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GnomAD4 genome ? AF: 0.114 AC: 17326AN: 152102Hom.: 1932 Cov.: 32 AF XY: 0.120 AC XY: 8952AN XY: 74326
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at