Genetic Variant CGB3:p.Cys120* (chr19-49023024-G-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_000737.5(CGB3):c.360C>A(p.Cys120*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. C120C) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0000075 ( 0 hom., cov: 17)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CGB3
NM_000737.5 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

0 publications found

Variant links:

Genes affected

CGB3 (HGNC:1886): (chorionic gonadotropin subunit beta 3) This gene is a member of the glycoprotein hormone beta chain family and encodes the beta 3 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]

CGB3 links:

ENSG00000267335 (HGNC:):

ENSG00000267335 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CGB3	NM_000737.5 link	c.360C>A	p.Cys120*	stop_gained	Exon 3 of 3	ENST00000357383.4	NP_000728.1	P0DN86-1A0A0F7RQP8
LOC124904738	XR_007067288.1 link	n.*209G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CGB3	ENST00000357383.4 link	c.360C>A	p.Cys120*	stop_gained	Exon 3 of 3	1	NM_000737.5	ENSP00000349954.2	P0DN86-1
ENSG00000267335	ENST00000591656.1 link	c.318C>A	p.Cys106*	stop_gained	Exon 3 of 3	2		ENSP00000466140.1	K7ELM3
ENSG00000267335	ENST00000604577.1 link	c.*122C>A		downstream_gene_variant		1		ENSP00000474022.1	S4R385

Frequencies

GnomAD3 genomes

AF:

0.00000746

AC:

AN:

134042

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000208

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

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1383120

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

685958

African (AFR)

AF:

0.00

AC:

AN:

30788

American (AMR)

AF:

0.00

AC:

AN:

34610

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23674

East Asian (EAS)

AF:

0.00

AC:

AN:

39020

South Asian (SAS)

AF:

0.00

AC:

AN:

79552

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49718

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3848

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1064714

Other (OTH)

AF:

0.00

AC:

AN:

57196

GnomAD4 genome

AF:

0.00000745

AC:

AN:

134142

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

64290

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

35292

American (AMR)

AF:

0.00

AC:

AN:

12658

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3284

East Asian (EAS)

AF:

0.000208

AC:

AN:

4800

South Asian (SAS)

AF:

0.00

AC:

AN:

3838

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9136

Middle Eastern (MID)

AF:

0.00

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

62252

Other (OTH)

AF:

0.00

AC:

AN:

1788

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.51

BayesDel_noAF

Pathogenic

0.49

CADD

Benign

(source)

DANN

Benign

0.97

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.15

PhyloP100

-1.0

Vest4

0.85

GERP RS

-2.0

Mutation Taster

=136/64

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over