rs4666865

Variant summary

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

The ENST00000295113.5(FRZB):​c.*1485T>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 0.321 in 152,056 control chromosomes in the GnomAD database, including 9,215 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 0.32 ( 9214 hom., cov: 32)
Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

FRZB
ENST00000295113.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.978
Variant links:
Genes affected
FRZB (HGNC:3959): (frizzled related protein) The protein encoded by this gene is a secreted protein that is involved in the regulation of bone development. Defects in this gene are a cause of female-specific osteoarthritis (OA) susceptibility. [provided by RefSeq, Apr 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FRZBNM_001463.4 linkuse as main transcriptc.*1485T>C 3_prime_UTR_variant 6/6 ENST00000295113.5 NP_001454.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FRZBENST00000295113.5 linkuse as main transcriptc.*1485T>C 3_prime_UTR_variant 6/61 NM_001463.4 ENSP00000295113 P1

Frequencies

GnomAD3 genomes
AF:
0.321
AC:
48761
AN:
151936
Hom.:
9214
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.127
Gnomad AMI
AF:
0.419
Gnomad AMR
AF:
0.454
Gnomad ASJ
AF:
0.414
Gnomad EAS
AF:
0.155
Gnomad SAS
AF:
0.395
Gnomad FIN
AF:
0.334
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.407
Gnomad OTH
AF:
0.348
GnomAD4 exome
AF:
1.00
AC:
2
AN:
2
Hom.:
1
Cov.:
0
AF XY:
1.00
AC XY:
2
AN XY:
2
show subpopulations
Gnomad4 NFE exome
AF:
1.00
GnomAD4 genome
AF:
0.321
AC:
48771
AN:
152054
Hom.:
9214
Cov.:
32
AF XY:
0.320
AC XY:
23748
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.127
Gnomad4 AMR
AF:
0.454
Gnomad4 ASJ
AF:
0.414
Gnomad4 EAS
AF:
0.155
Gnomad4 SAS
AF:
0.397
Gnomad4 FIN
AF:
0.334
Gnomad4 NFE
AF:
0.407
Gnomad4 OTH
AF:
0.343
Alfa
AF:
0.391
Hom.:
6155
Bravo
AF:
0.318
Asia WGS
AF:
0.256
AC:
889
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.5
DANN
Benign
0.33

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.

Other links and lift over

dbSNP: rs4666865; hg19: chr2-183698091; API