Genetic Variant FZD1:c.-94C>G (chr7-91264787-C-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_003505.2(FZD1):c.-94C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 817,494 control chromosomes in the GnomAD database, including 142,198 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 0.61 ( 28513 hom., cov: 33)

Exomes 𝑓: 0.58 ( 113685 hom. )

Consequence

FZD1
NM_003505.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.660

Publications

17 publications found

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003505.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD1	NM_003505.2	MANE Select	c.-94C>G		5_prime_UTR	Exon 1 of 1	NP_003496.1	Q9UP38

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD1	ENST00000287934.4	TSL:6 MANE Select	c.-94C>G		5_prime_UTR	Exon 1 of 1	ENSP00000287934.2	Q9UP38

Frequencies

GnomAD3 genomes

AF:

0.609

AC:

92389

AN:

151798

Hom.:

28510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.700

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.609

Gnomad MID

AF:

0.526

Gnomad NFE

AF:

0.586

Gnomad OTH

AF:

0.587

GnomAD4 exome

AF:

0.583

AC:

387806

AN:

665588

Hom.:

113685

Cov.:

AF XY:

0.582

AC XY:

188266

AN XY:

323488

show subpopulations

African (AFR)

AF:

0.700

AC:

10497

AN:

15000

American (AMR)

AF:

0.604

AC:

4716

AN:

7812

Ashkenazi Jewish (ASJ)

AF:

0.543

AC:

6324

AN:

11656

East Asian (EAS)

AF:

0.525

AC:

12739

AN:

24268

South Asian (SAS)

AF:

0.445

AC:

5877

AN:

13218

European-Finnish (FIN)

AF:

0.610

AC:

13144

AN:

21562

Middle Eastern (MID)

AF:

0.500

AC:

1049

AN:

2100

European-Non Finnish (NFE)

AF:

0.586

AC:

316389

AN:

539992

Other (OTH)

AF:

0.569

AC:

17071

AN:

29980

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

8339

16679

25018

33358

41697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8680

17360

26040

34720

43400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.608

AC:

92418

AN:

151906

Hom.:

28513

Cov.:

AF XY:

0.605

AC XY:

44941

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.699

AC:

28993

AN:

41488

American (AMR)

AF:

0.563

AC:

8599

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

1850

AN:

3472

East Asian (EAS)

AF:

0.522

AC:

2672

AN:

5118

South Asian (SAS)

AF:

0.459

AC:

2215

AN:

4826

European-Finnish (FIN)

AF:

0.609

AC:

6441

AN:

10574

Middle Eastern (MID)

AF:

0.528

AC:

152

AN:

288

European-Non Finnish (NFE)

AF:

0.586

AC:

39729

AN:

67838

Other (OTH)

AF:

0.580

AC:

1225

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1904

3809

5713

7618

9522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.496

Hom.:

1492

Bravo

AF:

0.614

Asia WGS

AF:

0.485

AC:

1669

AN:

3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

0.66

PromoterAI

0.027

Neutral

(source)

Mutation Taster

=296/4

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over