Variant rs3750145 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003505.2(FZD1):c.*692T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 167,144 control chromosomes in the GnomAD database, including 2,210 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 0.14 ( 1770 hom., cov: 33)

Exomes 𝑓: 0.24 ( 440 hom. )

Consequence

FZD1
NM_003505.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.799

Variant links:

Genes affected

FZD1 (HGNC:4038): (frizzled class receptor 1) Members of the 'frizzled' gene family encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. The FZD1 protein contains a signal peptide, a cysteine-rich domain in the N-terminal extracellular region, 7 transmembrane domains, and a C-terminal PDZ domain-binding motif. The FZD1 transcript is expressed in various tissues. [provided by RefSeq, Jul 2008]

FZD1 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FZD1	NM_003505.2 link	c.*692T>C		3_prime_UTR_variant	1/1	ENST00000287934.4	NP_003496.1	Q9UP38

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FZD1	ENST00000287934.4 link	c.*692T>C		3_prime_UTR_variant	1/1	6	NM_003505.2	ENSP00000287934.2		Q9UP38

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21904

AN:

152016

Hom.:

1768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0824

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.155

GnomAD4 exome

AF:

0.244

AC:

3659

AN:

15010

Hom.:

440

Cov.:

AF XY:

0.244

AC XY:

1749

AN XY:

7160

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.100

Gnomad4 FIN exome

AF:

0.245

Gnomad4 NFE exome

AF:

0.170

Gnomad4 OTH exome

AF:

0.240

GnomAD4 genome

AF:

0.144

AC:

21906

AN:

152134

Hom.:

1770

Cov.:

AF XY:

0.147

AC XY:

10914

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0823

Gnomad4 AMR

AF:

0.131

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.205

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.149

Hom.:

477

Bravo

AF:

0.134

Asia WGS

AF:

0.179

AC:

621

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.5

DANN

Benign

0.72

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