rs236140

Variant names:

• chr20-5911226-A-C
• rs236140
• ENST00000966395.1:c.-408A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-5911226-A-C
• chr20-5911226-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000966395.1(CHGB):​c.-408A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,058 control chromosomes in the GnomAD database, including 11,968 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 0.38 (11968 hom., cov: 32)
• Consequence: CHGB ENST00000966395.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000966395.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHGB	ENST00000966395.1		c.-408A>C		upstream_gene	N/A	ENSP00000636454.1
	CHGB	ENST00000966394.1		c.-408A>C		upstream_gene	N/A	ENSP00000636453.1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58289 AN: 151938 Hom.: 11952 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.380

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.384 AC: 58353 AN: 152058 Hom.: 11968 Cov.: 32 AF XY: 0.391 AC XY: 29054 AN XY: 74344

African (AFR) AF: 0.259 AC: 10747 AN: 41486

American (AMR) AF: 0.472 AC: 7205 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1324 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3425 AN: 5164

South Asian (SAS) AF: 0.476 AC: 2290 AN: 4808

European-Finnish (FIN) AF: 0.441 AC: 4664 AN: 10576

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27426 AN: 67960

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.376 Hom.: 1604

Bravo AF: 0.380

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.7
DANN	Benign	0.37
PhyloP100		-0.63
PromoterAI		0.031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs236140; hg19: chr20-5891872;