chr1-109250113-A-ACGC
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1
The NM_001408.3(CELSR2):c.47_49dup(p.Pro16dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 1,512,846 control chromosomes in the GnomAD database, including 343,325 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.64 ( 31205 hom., cov: 0)
Exomes 𝑓: 0.68 ( 312120 hom. )
Consequence
CELSR2
NM_001408.3 inframe_insertion
NM_001408.3 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.00700
Genes affected
CELSR2 (HGNC:3231): (cadherin EGF LAG seven-pass G-type receptor 2) The protein encoded by this gene is a member of the flamingo subfamily, part of the cadherin superfamily. The flamingo subfamily consists of nonclassic-type cadherins; a subpopulation that does not interact with catenins. The flamingo cadherins are located at the plasma membrane and have nine cadherin domains, seven epidermal growth factor-like repeats and two laminin A G-type repeats in their ectodomain. They also have seven transmembrane domains, a characteristic unique to this subfamily. It is postulated that these proteins are receptors involved in contact-mediated communication, with cadherin domains acting as homophilic binding regions and the EGF-like domains involved in cell adhesion and receptor-ligand interactions. The specific function of this particular member has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001408.3. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
Variant 1-109250113-A-ACGC is Benign according to our data. Variant chr1-109250113-A-ACGC is described in ClinVar as [Benign]. Clinvar id is 767684.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELSR2 | NM_001408.3 | c.47_49dup | p.Pro16dup | inframe_insertion | 1/34 | ENST00000271332.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELSR2 | ENST00000271332.4 | c.47_49dup | p.Pro16dup | inframe_insertion | 1/34 | 1 | NM_001408.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.636 AC: 95904AN: 150714Hom.: 31199 Cov.: 0
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GnomAD3 exomes AF: 0.638 AC: 109673AN: 171874Hom.: 34708 AF XY: 0.642 AC XY: 62857AN XY: 97928
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GnomAD4 exome AF: 0.680 AC: 926789AN: 1362022Hom.: 312120 Cov.: 60 AF XY: 0.679 AC XY: 459696AN XY: 676698
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GnomAD4 genome ? AF: 0.636 AC: 95950AN: 150824Hom.: 31205 Cov.: 0 AF XY: 0.633 AC XY: 46626AN XY: 73644
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at