rs1330691
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003408.3(ZFP37):c.349+1025G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,848 control chromosomes in the GnomAD database, including 23,942 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 0.56 ( 23942 hom., cov: 31)
Consequence
ZFP37
NM_003408.3 intron
NM_003408.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.453
Genes affected
ZFP37 (HGNC:12863): (ZFP37 zinc finger protein) This gene encodes a transcription factor that belongs to a large family of zinc finger proteins. A similar protein in mouse is thought to play a role in regulating the structures of the nucleolus and centromere in neurons. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFP37 | NM_003408.3 | c.349+1025G>C | intron_variant | ENST00000374227.8 | |||
ZFP37 | NM_001282515.2 | c.394+1025G>C | intron_variant | ||||
ZFP37 | NM_001282518.2 | c.352+1025G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFP37 | ENST00000374227.8 | c.349+1025G>C | intron_variant | 1 | NM_003408.3 | ||||
ZFP37 | ENST00000555206.5 | c.352+1025G>C | intron_variant | 1 | |||||
ZFP37 | ENST00000553380.1 | c.394+1025G>C | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.559 AC: 84824AN: 151730Hom.: 23912 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.559 AC: 84910AN: 151848Hom.: 23942 Cov.: 31 AF XY: 0.565 AC XY: 41908AN XY: 74216
GnomAD4 genome
?
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84910
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151848
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31
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41908
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74216
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2366
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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