2-130592943-C-T

Variant names:

• chr2-130592943-C-T
• rs587780887
• NM_032545.4:c.606G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001270420.2(CFC1):​c.491G>A​(p.Trp164*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 7)
• Consequence: CFC1 NM_001270420.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFC1	NM_032545.4	c.606G>A	p.Leu202Leu	synonymous_variant	Exon 6 of 6	ENST00000259216.6	NP_115934.1
CFC1	NM_001270420.2	c.491G>A	p.Trp164*	stop_gained	Exon 5 of 5		NP_001257349.1
CFC1	NM_001270421.2	c.381G>A	p.Leu127Leu	synonymous_variant	Exon 4 of 4		NP_001257350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFC1	ENST00000259216.6	c.606G>A	p.Leu202Leu	synonymous_variant	Exon 6 of 6	1	NM_032545.4	ENSP00000259216.5
CFC1	ENST00000615342.4	c.491G>A	p.Trp164*	stop_gained	Exon 5 of 5	5		ENSP00000480526.1
CFC1	ENST00000621673.4	c.381G>A	p.Leu127Leu	synonymous_variant	Exon 4 of 4	2		ENSP00000480843.1

Frequencies

GnomAD3 genomes Cov.: 7

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.78
FATHMM_MKL	Benign	0.00084	N
Vest4		0.26
GERP RS		-3.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs587780887; hg19: chr2-131350516;