chr2-182838453-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001463.4(FRZB):c.753T>C(p.Asn251=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,612,902 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000030 ( 1 hom. )
Consequence
FRZB
NM_001463.4 synonymous
NM_001463.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.30
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 2-182838453-A-G is Benign according to our data. Variant chr2-182838453-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3039181.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.3 with no splicing effect.
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRZB | NM_001463.4 | c.753T>C | p.Asn251= | synonymous_variant | 4/6 | ENST00000295113.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRZB | ENST00000295113.5 | c.753T>C | p.Asn251= | synonymous_variant | 4/6 | 1 | NM_001463.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152006Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250722Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135474
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GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460778Hom.: 1 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 726714
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74388
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FRZB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at