rs2294239

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000544604.7(ZNRF3):​c.2768-90A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

ZNRF3
ENST00000544604.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.29
Variant links:
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNRF3NM_001206998.2 linkuse as main transcriptc.2768-90A>C intron_variant ENST00000544604.7 NP_001193927.1
ZNRF3NM_032173.4 linkuse as main transcriptc.2468-90A>C intron_variant NP_115549.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNRF3ENST00000544604.7 linkuse as main transcriptc.2768-90A>C intron_variant 1 NM_001206998.2 ENSP00000443824 A2Q9ULT6-1
ZNRF3ENST00000406323.3 linkuse as main transcriptc.2468-90A>C intron_variant 1 ENSP00000384553 P2Q9ULT6-2
ZNRF3ENST00000402174.5 linkuse as main transcriptc.2468-90A>C intron_variant 2 ENSP00000384456 P2Q9ULT6-2

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.034
DANN
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2294239; hg19: chr22-29449477; API