rs1226749
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020883.2(ZSWIM5):c.595+32942A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,160 control chromosomes in the GnomAD database, including 2,665 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 0.16 ( 2665 hom., cov: 32)
Consequence
ZSWIM5
NM_020883.2 intron
NM_020883.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0960
Genes affected
ZSWIM5 (HGNC:29299): (zinc finger SWIM-type containing 5) Predicted to enable zinc ion binding activity. Located in extracellular space. [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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSWIM5 | NM_020883.2 | c.595+32942A>G | intron_variant | ENST00000359600.6 | NP_065934.1 | |||
ZSWIM5 | XM_047426192.1 | c.595+32942A>G | intron_variant | XP_047282148.1 | ||||
ZSWIM5 | XM_011541861.4 | c.595+32942A>G | intron_variant | XP_011540163.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZSWIM5 | ENST00000359600.6 | c.595+32942A>G | intron_variant | 1 | NM_020883.2 | ENSP00000352614.5 | ||||
ZSWIM5 | ENST00000464588.1 | n.228-84577A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.160 AC: 24350AN: 152042Hom.: 2665 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.160 AC: 24355AN: 152160Hom.: 2665 Cov.: 32 AF XY: 0.156 AC XY: 11598AN XY: 74406
GnomAD4 genome
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32
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11598
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74406
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160
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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