NM_033183.3:c.450T>C

Variant names:

• chr19-49047703-A-G
• rs71352726
• NM_033183.3:c.450T>C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_033183.3(CGB8):​c.450T>C​(p.Ser150Ser) 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 0.0042 (0 hom., cov: 28)
  • Exomes 𝑓: 0.000067 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: CGB8 NM_033183.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

CGB8 (HGNC:16453): (chorionic gonadotropin subunit beta 8) This gene is a member of the glycoprotein hormone beta chain family and encodes the beta 8 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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BP7: Synonymous conserved (PhyloP=0.042 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CGB8	NM_033183.3	c.450T>C	p.Ser150Ser	synonymous_variant	Exon 3 of 3	ENST00000448456.4	NP_149439.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CGB8	ENST00000448456.4	c.450T>C	p.Ser150Ser	synonymous_variant	Exon 3 of 3	1	NM_033183.3	ENSP00000403649.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 616 AN: 147344 Hom.: 0 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00186

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.00539

GnomAD3 exomes AF: 0.000154 AC: 11 AN: 71616 Hom.: 0 AF XY: 0.000169 AC XY: 6 AN XY: 35420

Gnomad AFR exome AF: 0.000707

Gnomad AMR exome AF: 0.000182

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000361

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000754

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000673 AC: 98 AN: 1457028 Hom.: 1 Cov.: 64 AF XY: 0.0000552 AC XY: 40 AN XY: 724838

Gnomad4 AFR exome AF: 0.00182

Gnomad4 AMR exome AF: 0.0000673

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000465

Gnomad4 FIN exome AF: 0.0000188

Gnomad4 NFE exome AF: 0.0000216

Gnomad4 OTH exome AF: 0.0000999

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00418 AC: 616 AN: 147452 Hom.: 0 Cov.: 28 AF XY: 0.00411 AC XY: 297 AN XY: 72250

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.00185

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000390

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.00533

Alfa AF: 0.0000749 Hom.: 0

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	0.30

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: rs71352726; hg19: chr19-49550960; COSMIC: COSV56822943; COSMIC: COSV56822943;