2-207767372-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003468.4(FZD5):c.1368C>T(p.Leu456=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000765 in 1,612,660 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00074 ( 7 hom. )
Consequence
FZD5
NM_003468.4 synonymous
NM_003468.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.458
Genes affected
FZD5 (HGNC:4043): (frizzled class receptor 5) Members of the 'frizzled' gene family encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. The FZD5 protein is believed to be the receptor for the Wnt5A ligand. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 2-207767372-G-A is Benign according to our data. Variant chr2-207767372-G-A is described in ClinVar as [Benign]. Clinvar id is 740988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.458 with no splicing effect.
BS2
High AC in GnomAd4 at 152 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FZD5 | NM_003468.4 | c.1368C>T | p.Leu456= | synonymous_variant | 2/2 | ENST00000295417.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FZD5 | ENST00000295417.4 | c.1368C>T | p.Leu456= | synonymous_variant | 2/2 | 1 | NM_003468.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000998 AC: 152AN: 152248Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00104 AC: 257AN: 247574Hom.: 2 AF XY: 0.00100 AC XY: 135AN XY: 134816
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GnomAD4 exome AF: 0.000740 AC: 1081AN: 1460294Hom.: 7 Cov.: 32 AF XY: 0.000790 AC XY: 574AN XY: 726514
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GnomAD4 genome AF: 0.000998 AC: 152AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.00109 AC XY: 81AN XY: 74514
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
FZD5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
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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