NM_001385261.1:c.327A>G

Variant names:

• chr19-49054462-T-C
• rs780960921
• NM_001385261.1:c.327A>G

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001385261.1(CGB7):​c.327A>G​(p.Gln109Gln) variant causes a synonymous 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: 𝑓 0.000014 (0 hom., cov: 20)
  • Exomes 𝑓: 0.000028 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CGB7 NM_001385261.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• 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: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP7: Synonymous conserved (PhyloP=0.719 with no splicing effect.

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.327A>G	p.Gln109Gln	synonymous	Exon 5 of 5	NP_001372190.1	P0DN87
	CGB7	NM_033142.2		c.327A>G	p.Gln109Gln	synonymous	Exon 5 of 5	NP_149133.1	P0DN87

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CGB7	ENST00000684222.1	MANE Select	c.327A>G	p.Gln109Gln	synonymous	Exon 5 of 5	ENSP00000507822.1	P0DN87
	CGB7	ENST00000596965.5	TSL:2	c.327A>G	p.Gln109Gln	synonymous	Exon 5 of 5	ENSP00000469076.1	P0DN87
	CGB7	ENST00000597853.5	TSL:2	c.327A>G	p.Gln109Gln	synonymous	Exon 5 of 5	ENSP00000470813.1	P0DN87

Frequencies

GnomAD3 genomes AF: 0.0000140 AC: 2 AN: 142388 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.0000514

Gnomad AMI 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

GnomAD2 exomes AF: 0.0000328 AC: 3 AN: 91566 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000208

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000277 AC: 40 AN: 1445390 Hom.: 0 Cov.: 34 AF XY: 0.0000292 AC XY: 21 AN XY: 718410

African (AFR) AF: 0.00 AC: 0 AN: 33278

American (AMR) AF: 0.0000228 AC: 1 AN: 43944

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25756

East Asian (EAS) AF: 0.0000506 AC: 2 AN: 39502

South Asian (SAS) AF: 0.0000352 AC: 3 AN: 85214

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52790

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4108

European-Non Finnish (NFE) AF: 0.0000309 AC: 34 AN: 1101156

Other (OTH) AF: 0.00 AC: 0 AN: 59642

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000140 AC: 2 AN: 142388 Hom.: 0 Cov.: 20 AF XY: 0.0000146 AC XY: 1 AN XY: 68628

African (AFR) AF: 0.0000514 AC: 2 AN: 38946

American (AMR) AF: 0.00 AC: 0 AN: 14048

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3372

East Asian (EAS) AF: 0.00 AC: 0 AN: 4782

South Asian (SAS) AF: 0.00 AC: 0 AN: 4080

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9492

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 308

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64588

Other (OTH) AF: 0.00 AC: 0 AN: 1892

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.21
PhyloP100		0.72

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

Other links and lift over

dbSNP: rs780960921; hg19: chr19-49557719;