chr19-49054626-A-G

Position:

• chr19-49054626-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001385261.1(CGB7):​c.184-21T>C variant causes a intron 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 0.048 (91 hom., cov: 17)
  • Exomes 𝑓: 0.087 (7210 hom.)
  • Failed GnomAD Quality Control
• Consequence: CGB7 NM_001385261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CGB7	NM_001385261.1	c.184-21T>C		intron_variant		ENST00000684222.1	NP_001372190.1
CGB7	NM_033142.2	c.184-21T>C		intron_variant			NP_149133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CGB7	ENST00000684222.1	c.184-21T>C		intron_variant			NM_001385261.1	ENSP00000507822.1
CGB7	ENST00000596965.5	c.184-21T>C		intron_variant		2		ENSP00000469076.1
CGB7	ENST00000597853.5	c.184-21T>C		intron_variant		2		ENSP00000470813.1

Frequencies

GnomAD3 genomes AF: 0.0483 AC: 5521 AN: 114288 Hom.: 91 Cov.: 17

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.0118

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0699

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0523

GnomAD3 exomes AF: 0.151 AC: 8413 AN: 55862 Hom.: 746 AF XY: 0.157 AC XY: 4403 AN XY: 28118

Gnomad AFR exome AF: 0.128

Gnomad AMR exome AF: 0.104

Gnomad ASJ exome AF: 0.127

Gnomad EAS exome AF: 0.154

Gnomad SAS exome AF: 0.157

Gnomad FIN exome AF: 0.202

Gnomad NFE exome AF: 0.177

Gnomad OTH exome AF: 0.158

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0868 AC: 73177 AN: 843144 Hom.: 7210 Cov.: 13 AF XY: 0.0895 AC XY: 37717 AN XY: 421310

Gnomad4 AFR exome AF: 0.0773

Gnomad4 AMR exome AF: 0.0609

Gnomad4 ASJ exome AF: 0.0882

Gnomad4 EAS exome AF: 0.0925

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.172

Gnomad4 NFE exome AF: 0.0803

Gnomad4 OTH exome AF: 0.0982

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0483 AC: 5520 AN: 114364 Hom.: 91 Cov.: 17 AF XY: 0.0442 AC XY: 2427 AN XY: 54930

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.0493

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0554

Gnomad4 OTH AF: 0.0523

Alfa AF: 0.0525 Hom.: 126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs34935416; hg19: chr19-49557883; COSMIC: COSV62281703; COSMIC: COSV62281703;