chr2-130598920-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_032545.4(CFC1):āc.63T>Cā(p.Asn21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.022 ( 1 hom., cov: 20)
Exomes š: 0.0026 ( 1 hom. )
Consequence
CFC1
NM_032545.4 synonymous
NM_032545.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.505
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 Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
Variant 2-130598920-A-G is Benign according to our data. Variant chr2-130598920-A-G is described in ClinVar as [Benign]. Clinvar id is 136732.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-130598920-A-G is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-0.505 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFC1 | NM_032545.4 | c.63T>C | p.Asn21= | synonymous_variant | 2/6 | ENST00000259216.6 | |
CFC1 | NM_001270420.2 | c.63T>C | p.Asn21= | synonymous_variant | 2/5 | ||
CFC1 | NM_001270421.2 | c.63T>C | p.Asn21= | synonymous_variant | 2/4 | ||
CFC1 | XM_011511486.4 | c.63T>C | p.Asn21= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFC1 | ENST00000259216.6 | c.63T>C | p.Asn21= | synonymous_variant | 2/6 | 1 | NM_032545.4 | P1 | |
CFC1 | ENST00000615342.4 | c.63T>C | p.Asn21= | synonymous_variant | 2/5 | 5 | |||
CFC1 | ENST00000621673.4 | c.63T>C | p.Asn21= | synonymous_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0218 AC: 2921AN: 133926Hom.: 1 Cov.: 20
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GnomAD4 exome AF: 0.00257 AC: 2523AN: 982112Hom.: 1 Cov.: 13 AF XY: 0.00214 AC XY: 1062AN XY: 495346
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GnomAD4 genome AF: 0.0219 AC: 2931AN: 134026Hom.: 1 Cov.: 20 AF XY: 0.0209 AC XY: 1350AN XY: 64460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2012 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at