Genetic Variant FZD7:c.*140C>T (chr2-202036512-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003507.2(FZD7):c.*140C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 697,022 control chromosomes in the GnomAD database, including 28,217 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 0.27 ( 5990 hom., cov: 33)

Exomes 𝑓: 0.27 ( 22227 hom. )

Consequence

FZD7
NM_003507.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Publications

15 publications found

Variant links:

Genes affected

FZD7 (HGNC:4045): (frizzled class receptor 7) Members of the 'frizzled' gene family encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. The FZD7 protein contains an N-terminal signal sequence, 10 cysteine residues typical of the cysteine-rich extracellular domain of Fz family members, 7 putative transmembrane domains, and an intracellular C-terminal tail with a PDZ domain-binding motif. FZD7 gene expression may downregulate APC function and enhance beta-catenin-mediated signals in poorly differentiated human esophageal carcinomas. [provided by RefSeq, Jul 2008]

FZD7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003507.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD7	NM_003507.2	MANE Select	c.*140C>T		3_prime_UTR	Exon 1 of 1	NP_003498.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD7	ENST00000286201.3	TSL:6 MANE Select	c.*140C>T		3_prime_UTR	Exon 1 of 1	ENSP00000286201.1

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41199

AN:

151930

Hom.:

5988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.00597

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.172

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.233

GnomAD4 exome

AF:

0.271

AC:

147693

AN:

544974

Hom.:

22227

Cov.:

AF XY:

0.263

AC XY:

73800

AN XY:

280088

show subpopulations

African (AFR)

AF:

0.258

AC:

3657

AN:

14178

American (AMR)

AF:

0.261

AC:

4814

AN:

18436

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

2412

AN:

14110

East Asian (EAS)

AF:

0.00246

AC:

AN:

31280

South Asian (SAS)

AF:

0.121

AC:

5198

AN:

42812

European-Finnish (FIN)

AF:

0.360

AC:

15848

AN:

44020

Middle Eastern (MID)

AF:

0.153

AC:

332

AN:

2166

European-Non Finnish (NFE)

AF:

0.310

AC:

108167

AN:

349210

Other (OTH)

AF:

0.250

AC:

7188

AN:

28762

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

5329

10658

15986

21315

26644

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1604

3208

4812

6416

8020

<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:

0.271

AC:

41230

AN:

152048

Hom.:

5990

Cov.:

AF XY:

0.268

AC XY:

19938

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.252

AC:

10451

AN:

41464

American (AMR)

AF:

0.261

AC:

3992

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

608

AN:

3472

East Asian (EAS)

AF:

0.00618

AC:

AN:

5180

South Asian (SAS)

AF:

0.108

AC:

520

AN:

4810

European-Finnish (FIN)

AF:

0.365

AC:

3848

AN:

10540

Middle Eastern (MID)

AF:

0.168

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.310

AC:

21075

AN:

67988

Other (OTH)

AF:

0.235

AC:

495

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1491

2981

4472

5962

7453

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.255

Hom.:

2600

Bravo

AF:

0.263

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.14

(source)

DANN

Benign

0.61

PhyloP100

-1.3

Mutation Taster

=100/0

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