Variant rs3178915 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001206998.2(ZNRF3):c.*3417A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,070 control chromosomes in the GnomAD database, including 23,587 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 0.55 ( 23587 hom., cov: 33)

Failed GnomAD Quality Control

Consequence

ZNRF3
NM_001206998.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.643

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]

ZNRF3 links:

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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=-0.49).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNRF3	NM_001206998.2 link	c.*3417A>G		3_prime_UTR_variant	9/9	ENST00000544604.7	NP_001193927.1
ZNRF3	NM_032173.4 link	c.*3417A>G		3_prime_UTR_variant	9/9		NP_115549.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNRF3	ENST00000544604.7 link	c.*3417A>G		3_prime_UTR_variant	9/9	1	NM_001206998.2	ENSP00000443824.2		Q9ULT6-1

Frequencies

GnomAD3 genomes

AF:

0.553

AC:

84001

AN:

151952

Hom.:

23542

Cov.:

show subpopulations

Gnomad AFR

AF:

0.610

Gnomad AMI

AF:

0.452

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.583

Gnomad EAS

AF:

0.616

Gnomad SAS

AF:

0.637

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.512

Gnomad OTH

AF:

0.549

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.553

AC:

84102

AN:

152070

Hom.:

23587

Cov.:

AF XY:

0.555

AC XY:

41216

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.611

Gnomad4 AMR

AF:

0.541

Gnomad4 ASJ

AF:

0.583

Gnomad4 EAS

AF:

0.616

Gnomad4 SAS

AF:

0.637

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.512

Gnomad4 OTH

AF:

0.551

Alfa

AF:

0.522

Hom.:

35751

Bravo

AF:

0.552

Asia WGS

AF:

0.640

AC:

2225

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

6.4

DANN

Benign

0.67

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over