Genetic Variant FZD1:c.-225C>G (chr7-91264656-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003505.2(FZD1):c.-225C>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 0.0000084 in 238,128 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000084 ( 0 hom. )

Consequence

FZD1
NM_003505.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

Publications

1 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FZD1	NM_003505.2 link	c.-225C>G		5_prime_UTR_variant	Exon 1 of 1	ENST00000287934.4	NP_003496.1	Q9UP38

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FZD1	ENST00000287934.4 link	c.-225C>G		5_prime_UTR_variant	Exon 1 of 1	6	NM_003505.2	ENSP00000287934.2		Q9UP38

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000840

AC:

AN:

238128

Hom.:

Cov.:

AF XY:

0.0000165

AC XY:

AN XY:

121152

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6708

American (AMR)

AF:

0.00

AC:

AN:

7052

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8714

East Asian (EAS)

AF:

0.00

AC:

AN:

21924

South Asian (SAS)

AF:

0.00

AC:

AN:

2248

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20756

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1238

European-Non Finnish (NFE)

AF:

0.0000130

AC:

AN:

153818

Other (OTH)

AF:

0.00

AC:

AN:

15670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

9.7

(source)

DANN

Benign

0.85

PhyloP100

-0.23

PromoterAI

0.060

Neutral

(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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over