rs10483153
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001206998.2(ZNRF3):c.426+19562A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0153 in 152,306 control chromosomes in the GnomAD database, including 46 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 0.015 ( 46 hom., cov: 32)
Consequence
ZNRF3
NM_001206998.2 intron
NM_001206998.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.596
Genes affected
ZNRF3 (HGNC:18126): (zinc and ring finger 3) Enables frizzled binding activity and ubiquitin-protein transferase activity. Involved in cellular protein metabolic process and negative regulation of Wnt signaling pathway. Is integral component of plasma membrane. [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=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0524 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNRF3 | NM_001206998.2 | c.426+19562A>G | intron_variant | ENST00000544604.7 | |||
ZNRF3 | NM_032173.4 | c.126+19562A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNRF3 | ENST00000544604.7 | c.426+19562A>G | intron_variant | 1 | NM_001206998.2 | A2 | |||
ZNRF3 | ENST00000406323.3 | c.126+19562A>G | intron_variant | 1 | P2 | ||||
ZNRF3-IT1 | ENST00000412798.1 | n.218-11401A>G | intron_variant, non_coding_transcript_variant | 5 | |||||
ZNRF3 | ENST00000402174.5 | c.126+19562A>G | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0153 AC: 2328AN: 152188Hom.: 44 Cov.: 32
GnomAD3 genomes
?
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2328
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152188
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0153 AC: 2337AN: 152306Hom.: 46 Cov.: 32 AF XY: 0.0177 AC XY: 1318AN XY: 74486
GnomAD4 genome
?
AF:
AC:
2337
AN:
152306
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32
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1318
AN XY:
74486
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Asia WGS
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162
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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