rs3806502
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000401392.5(ZRANB3):c.-185G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,194 control chromosomes in the GnomAD database, including 11,174 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 0.31 ( 11174 hom., cov: 32)
Exomes 𝑓: 0.094 ( 0 hom. )
Consequence
ZRANB3
ENST00000401392.5 5_prime_UTR
ENST00000401392.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.197
Genes affected
ZRANB3 (HGNC:25249): (zinc finger RANBP2-type containing 3) Enables ATP-dependent DNA/DNA annealing activity; K63-linked polyubiquitin modification-dependent protein binding activity; and endodeoxyribonuclease activity. Involved in several processes, including DNA metabolic process; DNA rewinding; and negative regulation of DNA recombination. Located in nuclear replication fork and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZRANB3 | NM_032143.4 | c.-8+424G>A | intron_variant | ENST00000264159.11 | |||
ZRANB3 | NM_001286569.1 | c.-1670G>A | 5_prime_UTR_variant | 1/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZRANB3 | ENST00000401392.5 | c.-185G>A | 5_prime_UTR_variant | 1/21 | 1 | A2 | |||
ZRANB3 | ENST00000536680.5 | c.-1670G>A | 5_prime_UTR_variant | 1/22 | 1 | ||||
ZRANB3 | ENST00000264159.11 | c.-8+424G>A | intron_variant | 1 | NM_032143.4 | P4 | |||
ZRANB3 | ENST00000452187.6 | n.73+424G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.307 AC: 46752AN: 152044Hom.: 11129 Cov.: 32
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GnomAD4 exome AF: 0.0938 AC: 3AN: 32Hom.: 0 Cov.: 0 AF XY: 0.0769 AC XY: 2AN XY: 26
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GnomAD4 genome ? AF: 0.308 AC: 46855AN: 152162Hom.: 11174 Cov.: 32 AF XY: 0.310 AC XY: 23079AN XY: 74394
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at