rs863223280
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5
The NM_032545.4(CFC1):c.362+18_362+19insAGGTGGGCACAGGGGTGCGC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CFC1
NM_032545.4 intron
NM_032545.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0490
Genes affected
CFC1 (HGNC:18292): (cryptic, EGF-CFC family member 1) This gene encodes a member of the epidermal growth factor (EGF)- Cripto, Frl-1, and Cryptic (CFC) family, which are involved in signalling during embryonic development. Proteins in this family share a variant EGF-like motif, a conserved cysteine-rich domain, and a C-terminal hydrophobic region. The protein encoded by this gene is necessary for patterning the left-right embryonic axis. Mutations in this gene are associated with defects in organ development, including autosomal visceral heterotaxy and congenital heart disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP5
?
Variant 2-130597849-C-CGCGCACCCCTGTGCCCACCT is Pathogenic according to our data. Variant chr2-130597849-C-CGCGCACCCCTGTGCCCACCT is described in ClinVar as [Pathogenic]. Clinvar id is 5190.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFC1 | NM_032545.4 | c.362+18_362+19insAGGTGGGCACAGGGGTGCGC | intron_variant | ENST00000259216.6 | |||
CFC1 | NM_001270420.2 | c.248-247_248-246insAGGTGGGCACAGGGGTGCGC | intron_variant | ||||
CFC1 | NM_001270421.2 | c.247+792_247+793insAGGTGGGCACAGGGGTGCGC | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFC1 | ENST00000259216.6 | c.362+18_362+19insAGGTGGGCACAGGGGTGCGC | intron_variant | 1 | NM_032545.4 | P1 | |||
CFC1 | ENST00000615342.4 | c.248-247_248-246insAGGTGGGCACAGGGGTGCGC | intron_variant | 5 | |||||
CFC1 | ENST00000621673.4 | c.247+792_247+793insAGGTGGGCACAGGGGTGCGC | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 genomes
?
Cov.:
0
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 664Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 324
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
664
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0
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0
AN XY:
324
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GnomAD4 genome ? Cov.: 0
GnomAD4 genome
?
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0
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Heterotaxy, visceral, 2, autosomal Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2002 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at