rs3808558

Positions:

• chr8-103312831-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003506.4(FZD6):​c.178-5759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 152,178 control chromosomes in the GnomAD database, including 1,166 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 0.095 (1166 hom., cov: 32)
• Consequence: FZD6 NM_003506.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

FZD6 (HGNC:4044): (frizzled class receptor 6) This gene represents a member of the 'frizzled' gene family, which encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. The protein encoded by this family member contains a signal peptide, a cysteine-rich domain in the N-terminal extracellular region, and seven transmembrane domains, but unlike other family members, this protein does not contain a C-terminal PDZ domain-binding motif. This protein functions as a negative regulator of the canonical Wnt/beta-catenin signaling cascade, thereby inhibiting the processes that trigger oncogenic transformation, cell proliferation, and inhibition of apoptosis. Alternative splicing results in multiple transcript variants, some of which do not encode a protein with a predicted signal peptide.[provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FZD6	NM_003506.4	c.178-5759G>A		intron_variant		ENST00000358755.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FZD6	ENST00000358755.5	c.178-5759G>A		intron_variant		1	NM_003506.4	P1

Frequencies

GnomAD3 genomes AF: 0.0950 AC: 14439 AN: 152060 Hom.: 1163 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0674

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0950 AC: 14461 AN: 152178 Hom.: 1166 Cov.: 32 AF XY: 0.0955 AC XY: 7107 AN XY: 74400

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0392

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.0674

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0699

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0723 Hom.: 248

Bravo AF: 0.0986

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.71

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

Other links and lift over

dbSNP: rs3808558; hg19: chr8-104325059;