2-182837942-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001463.4(FRZB):c.861+6C>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0046 in 1,608,016 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0048 ( 26 hom. )
Consequence
FRZB
NM_001463.4 splice_donor_region, intron
NM_001463.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0001893
2
Clinical Significance
Conservation
PhyloP100: 0.312
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 2-182837942-G-T is Benign according to our data. Variant chr2-182837942-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 719233.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 446 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRZB | NM_001463.4 | c.861+6C>A | splice_donor_region_variant, intron_variant | ENST00000295113.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRZB | ENST00000295113.5 | c.861+6C>A | splice_donor_region_variant, intron_variant | 1 | NM_001463.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00294 AC: 446AN: 151670Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00285 AC: 714AN: 250270Hom.: 1 AF XY: 0.00299 AC XY: 405AN XY: 135316
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GnomAD4 exome AF: 0.00478 AC: 6955AN: 1456228Hom.: 26 Cov.: 29 AF XY: 0.00464 AC XY: 3360AN XY: 724610
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GnomAD4 genome ? AF: 0.00294 AC: 446AN: 151788Hom.: 1 Cov.: 32 AF XY: 0.00293 AC XY: 217AN XY: 74170
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at