chr7-91264656-C-G

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

2

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]

Genome browser will be placed here

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
FZD1NM_003505.2 linkc.-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
FZD1ENST00000287934.4 linkc.-225C>G 5_prime_UTR_variant Exon 1 of 1 6 NM_003505.2 ENSP00000287934.2 Q9UP38

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000840
AC:
2
AN:
238128
Hom.:
0
Cov.:
2
AF XY:
0.0000165
AC XY:
2
AN XY:
121152
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
6708
American (AMR)
AF:
0.00
AC:
0
AN:
7052
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
8714
East Asian (EAS)
AF:
0.00
AC:
0
AN:
21924
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2248
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
20756
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1238
European-Non Finnish (NFE)
AF:
0.0000130
AC:
2
AN:
153818
Other (OTH)
AF:
0.00
AC:
0
AN:
15670
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0

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
DANN
Benign
0.85
PhyloP100
-0.23
PromoterAI
0.060
Neutral

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

Other links and lift over

dbSNP: rs2232156; hg19: chr7-90893971; API