dbSNP rs236155: CHGB:c.1957-68G>A (chr20-5924904-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001819.3(CHGB):c.1957-68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 914,172 control chromosomes in the GnomAD database, including 84,069 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 ( 17592 hom., cov: 32)

Exomes 𝑓: 0.41 ( 66477 hom. )

Consequence

CHGB
NM_001819.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.542

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHGB	NM_001819.3 link	c.1957-68G>A		intron_variant	Intron 4 of 4	ENST00000378961.9	NP_001810.2	P05060

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHGB	ENST00000378961.9 link	c.1957-68G>A		intron_variant	Intron 4 of 4	1	NM_001819.3	ENSP00000368244.4		P05060

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70805

AN:

151920

Hom.:

17560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.542

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.426

GnomAD4 exome

AF:

0.409

AC:

311495

AN:

762134

Hom.:

66477

AF XY:

0.407

AC XY:

163880

AN XY:

402836

show subpopulations

Gnomad4 AFR exome

AF:

0.625

Gnomad4 AMR exome

AF:

0.617

Gnomad4 ASJ exome

AF:

0.285

Gnomad4 EAS exome

AF:

0.531

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.419

Gnomad4 NFE exome

AF:

0.376

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.466

AC:

70895

AN:

152038

Hom.:

17592

Cov.:

AF XY:

0.469

AC XY:

34844

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.626

Gnomad4 AMR

AF:

0.507

Gnomad4 ASJ

AF:

0.285

Gnomad4 EAS

AF:

0.542

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.410

Hom.:

3893

Bravo

AF:

0.479

Asia WGS

AF:

0.543

AC:

1890

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.53

DANN

Benign

0.26

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