Genetic Variant NM_032545.4:c.260_267delGGCCGCGC (chr2-130597962-AGCGCGGCC-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_032545.4(CFC1):c.260_267delGGCCGCGC(p.Arg87LeufsTer28) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 1)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CFC1
NM_032545.4 frameshift

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.54

Publications

0 publications found

Variant links:

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]

CFC1 Gene-Disease associations (from GenCC):

heterotaxy, visceral, 2, autosomal
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

CFC1 links:

ENSG00000296255 (HGNC:):

ENSG00000296255 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032545.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CFC1	NM_032545.4	MANE Select	c.260_267delGGCCGCGC	p.Arg87LeufsTer28	frameshift	Exon 4 of 6	NP_115934.1	P0CG37
CFC1	NM_001270420.2		c.248-367_248-360delGGCCGCGC		intron	N/A	NP_001257349.1	A0A087WWV2
CFC1	NM_001270421.2		c.247+672_247+679delGGCCGCGC		intron	N/A	NP_001257350.1	A0A087WX98

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CFC1	ENST00000259216.6	TSL:1 MANE Select	c.260_267delGGCCGCGC	p.Arg87LeufsTer28	frameshift	Exon 4 of 6	ENSP00000259216.5	P0CG37
CFC1	ENST00000615342.4	TSL:5	c.248-367_248-360delGGCCGCGC		intron	N/A	ENSP00000480526.1	A0A087WWV2
CFC1	ENST00000621673.4	TSL:2	c.247+672_247+679delGGCCGCGC		intron	N/A	ENSP00000480843.1	A0A087WX98

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

2158

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

9898

Hom.:

AF XY:

0.00

AC XY:

AN XY:

4748

African (AFR)

AF:

0.00

AC:

AN:

146

American (AMR)

AF:

0.00

AC:

AN:

188

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

316

East Asian (EAS)

AF:

0.00

AC:

AN:

240

South Asian (SAS)

AF:

0.00

AC:

AN:

308

European-Finnish (FIN)

AF:

0.00

AC:

AN:

460

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

7494

Other (OTH)

AF:

0.00

AC:

AN:

704

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

2156

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

958

African (AFR)

AF:

0.00

AC:

AN:

300

American (AMR)

AF:

0.00

AC:

AN:

338

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

192

South Asian (SAS)

AF:

0.00

AC:

AN:

156

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1000

Other (OTH)

AF:

0.00

AC:

AN:

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.5

Mutation Taster

=55/145

disease causing (fs/PTC)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over