Variant rs2241802 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017412.4(FZD3):c.435A>G(p.Leu145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,612,640 control chromosomes in the GnomAD database, including 254,266 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 0.53 ( 22105 hom., cov: 30)

Exomes 𝑓: 0.56 ( 232161 hom. )

Consequence

FZD3
NM_017412.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250

Variant links:

Genes affected

FZD3 (HGNC:4041): (frizzled class receptor 3) This gene is a member of the frizzled gene family. Members of this family encode seven-transmembrane domain proteins that are receptors for the wingless type MMTV integration site family of signaling proteins. Most frizzled receptors are coupled to the beta-catenin canonical signaling pathway. The function of this protein is unknown, although it may play a role in mammalian hair follicle development. Alternative splicing results in multiple transcript variants. This gene is a susceptibility locus for schizophrenia. [provided by RefSeq, Dec 2010]

FZD3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=0.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FZD3	NM_017412.4 linkuse as main transcript	c.435A>G	p.Leu145=	synonymous_variant	5/8	ENST00000240093.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FZD3	ENST00000240093.8 linkuse as main transcript	c.435A>G	p.Leu145=	synonymous_variant	5/8	1	NM_017412.4	P1	Q9NPG1-1
FZD3	ENST00000537916.2 linkuse as main transcript	c.435A>G	p.Leu145=	synonymous_variant	4/7	2		P1	Q9NPG1-1

Frequencies

GnomAD3 genomes

AF:

0.533

AC:

80903

AN:

151738

Hom.:

22095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.574

Gnomad ASJ

AF:

0.637

Gnomad EAS

AF:

0.578

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.602

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.564

Gnomad OTH

AF:

0.549

GnomAD3 exomes

AF:

0.569

AC:

142861

AN:

250878

Hom.:

41138

AF XY:

0.577

AC XY:

78181

AN XY:

135604

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.553

Gnomad ASJ exome

AF:

0.629

Gnomad EAS exome

AF:

0.586

Gnomad SAS exome

AF:

0.629

Gnomad FIN exome

AF:

0.589

Gnomad NFE exome

AF:

0.569

Gnomad OTH exome

AF:

0.589

GnomAD4 exome

AF:

0.563

AC:

821803

AN:

1460784

Hom.:

232161

Cov.:

AF XY:

0.566

AC XY:

411269

AN XY:

726746

show subpopulations

Gnomad4 AFR exome

AF:

0.422

Gnomad4 AMR exome

AF:

0.555

Gnomad4 ASJ exome

AF:

0.626

Gnomad4 EAS exome

AF:

0.561

Gnomad4 SAS exome

AF:

0.628

Gnomad4 FIN exome

AF:

0.589

Gnomad4 NFE exome

AF:

0.559

Gnomad4 OTH exome

AF:

0.567

GnomAD4 genome

AF:

0.533

AC:

80952

AN:

151856

Hom.:

22105

Cov.:

AF XY:

0.538

AC XY:

39936

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.418

Gnomad4 AMR

AF:

0.574

Gnomad4 ASJ

AF:

0.637

Gnomad4 EAS

AF:

0.578

Gnomad4 SAS

AF:

0.635

Gnomad4 FIN

AF:

0.602

Gnomad4 NFE

AF:

0.564

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.565

Hom.:

56332

Bravo

AF:

0.525

Asia WGS

AF:

0.618

AC:

2146

AN:

3476

EpiCase

AF:

0.573

EpiControl

AF:

0.566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.9

DANN

Benign

0.80

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.

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