19-49054555-GT-AC

Variant names:

• chr19-49054555-GT-AC
• NM_001385261.1:c.233_234delACinsGT
• CGB7 p.Asn78Ser

Variant summary

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

The NM_001385261.1(CGB7):​c.233_234delACinsGT​(p.Asn78Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N78T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 18)
• Consequence: CGB7 NM_001385261.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 0 publications found

Genes affected

CGB7 (HGNC:16451): (chorionic gonadotropin subunit beta 7) This gene is a member of the glycoprotein hormone beta chain family and encodes the beta 7 subunit of chorionic gonadotropin (CG). Glycoprotein hormones are heterodimers consisting of a common alpha subunit and an unique beta subunit which confers biological specificity. CG is produced by the trophoblastic cells of the placenta and stimulates the ovaries to synthesize the steroids that are essential for the maintenance of pregnancy. The beta subunit of CG is encoded by 6 genes which are arranged in tandem and inverted pairs on chromosome 19q13.3 and contiguous with the luteinizing hormone beta subunit gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385261.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CGB7	NM_001385261.1	MANE Select	c.233_234delACinsGT	p.Asn78Ser	missense	N/A	NP_001372190.1	P0DN87
	CGB7	NM_033142.2		c.233_234delACinsGT	p.Asn78Ser	missense	N/A	NP_149133.1	P0DN87

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CGB7	ENST00000684222.1	MANE Select	c.233_234delACinsGT	p.Asn78Ser	missense	N/A	ENSP00000507822.1	P0DN87
	CGB7	ENST00000596965.5	TSL:2	c.233_234delACinsGT	p.Asn78Ser	missense	N/A	ENSP00000469076.1	P0DN87
	CGB7	ENST00000597853.5	TSL:2	c.233_234delACinsGT	p.Asn78Ser	missense	N/A	ENSP00000470813.1	P0DN87

Frequencies

GnomAD3 genomes Cov.: 18

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 18

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-49557812;