rs12610873
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001367834.3(ZSWIM4):c.*723G>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 0.333 in 152,106 control chromosomes in the GnomAD database, including 8,556 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 0.33 ( 8534 hom., cov: 29)
Exomes 𝑓: 0.40 ( 22 hom. )
Consequence
ZSWIM4
NM_001367834.3 3_prime_UTR
NM_001367834.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.623
Genes affected
ZSWIM4 (HGNC:25704): (zinc finger SWIM-type containing 4) Predicted to enable zinc ion binding activity. Predicted to be part of Cul2-RING ubiquitin ligase complex. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZSWIM4 | NM_001367834.3 | c.*723G>A | 3_prime_UTR_variant | 14/14 | ENST00000590508.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZSWIM4 | ENST00000590508.6 | c.*723G>A | 3_prime_UTR_variant | 14/14 | 2 | NM_001367834.3 | P1 | ||
MIR23AHG | ENST00000587762.2 | n.11156C>T | non_coding_transcript_exon_variant | 1/1 | |||||
ZSWIM4 | ENST00000254323.6 | c.*723G>A | 3_prime_UTR_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.333 AC: 50567AN: 151646Hom.: 8532 Cov.: 29
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GnomAD4 exome AF: 0.398 AC: 137AN: 344Hom.: 22 Cov.: 0 AF XY: 0.399 AC XY: 87AN XY: 218
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GnomAD4 genome ? AF: 0.333 AC: 50586AN: 151762Hom.: 8534 Cov.: 29 AF XY: 0.332 AC XY: 24625AN XY: 74114
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ClinVar
Not reported inComputational scores
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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