Variant rs236153 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001819.3(CHGB):c.1104A>G(p.Glu368Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,613,492 control chromosomes in the GnomAD database, including 135,307 homozygotes. 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 0.47 ( 17602 hom., cov: 31)

Exomes 𝑓: 0.39 ( 117705 hom. )

Consequence

CHGB
NM_001819.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.639

Variant links:

Genes affected

CHGB (HGNC:1930): (chromogranin B) This gene encodes a tyrosine-sulfated secretory protein abundant in peptidergic endocrine cells and neurons. This protein may serve as a precursor for regulatory peptides. [provided by RefSeq, Jan 2009]

CHGB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=-0.639 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHGB	NM_001819.3 link	c.1104A>G	p.Glu368Glu	synonymous_variant	4/5	ENST00000378961.9	NP_001810.2	P05060

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHGB	ENST00000378961.9 link	c.1104A>G	p.Glu368Glu	synonymous_variant	4/5	1	NM_001819.3	ENSP00000368244.4		P05060

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70739

AN:

151758

Hom.:

17568

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.455

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.334

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.426

GnomAD3 exomes

AF:

0.448

AC:

112549

AN:

250954

Hom.:

27198

AF XY:

0.435

AC XY:

58944

AN XY:

135638

show subpopulations

Gnomad AFR exome

AF:

0.627

Gnomad AMR exome

AF:

0.635

Gnomad ASJ exome

AF:

0.288

Gnomad EAS exome

AF:

0.558

Gnomad SAS exome

AF:

0.443

Gnomad FIN exome

AF:

0.415

Gnomad NFE exome

AF:

0.373

Gnomad OTH exome

AF:

0.403

GnomAD4 exome

AF:

0.395

AC:

576723

AN:

1461614

Hom.:

117705

Cov.:

AF XY:

0.394

AC XY:

286640

AN XY:

727100

show subpopulations

Gnomad4 AFR exome

AF:

0.627

Gnomad4 AMR exome

AF:

0.620

Gnomad4 ASJ exome

AF:

0.284

Gnomad4 EAS exome

AF:

0.533

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.372

Gnomad4 OTH exome

AF:

0.398

GnomAD4 genome

AF:

0.466

AC:

70831

AN:

151878

Hom.:

17602

Cov.:

AF XY:

0.469

AC XY:

34807

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.626

Gnomad4 AMR

AF:

0.507

Gnomad4 ASJ

AF:

0.284

Gnomad4 EAS

AF:

0.542

Gnomad4 SAS

AF:

0.454

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.389

Hom.:

22033

Bravo

AF:

0.479

Asia WGS

AF:

0.544

AC:

1892

AN:

3478

EpiCase

AF:

0.366

EpiControl

AF:

0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.58

DANN

Benign

0.55

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over