rs236155

Variant names:

• chr20-5924904-G-A
• rs236155
• NM_001819.3:c.1957-68G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-5924904-G-A
• chr20-5924904-G-C
• chr20-5924904-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001819.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHGB	NM_001819.3	MANE Select	c.1957-68G>A		intron	N/A	NP_001810.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHGB	ENST00000378961.9	TSL:1 MANE Select	c.1957-68G>A		intron	N/A	ENSP00000368244.4

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70805 AN: 151920 Hom.: 17560 Cov.: 32

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

African (AFR) AF: 0.625 AC: 12375 AN: 19788

American (AMR) AF: 0.617 AC: 23509 AN: 38124

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 5878 AN: 20616

East Asian (EAS) AF: 0.531 AC: 18926 AN: 35628

South Asian (SAS) AF: 0.439 AC: 29581 AN: 67430

European-Finnish (FIN) AF: 0.419 AC: 20476 AN: 48912

Middle Eastern (MID) AF: 0.365 AC: 1594 AN: 4372

European-Non Finnish (NFE) AF: 0.376 AC: 184364 AN: 490326

Other (OTH) AF: 0.400 AC: 14792 AN: 36938

GnomAD4 genome AF: 0.466 AC: 70895 AN: 152038 Hom.: 17592 Cov.: 32 AF XY: 0.469 AC XY: 34844 AN XY: 74324

African (AFR) AF: 0.626 AC: 25941 AN: 41444

American (AMR) AF: 0.507 AC: 7753 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3470

East Asian (EAS) AF: 0.542 AC: 2803 AN: 5170

South Asian (SAS) AF: 0.453 AC: 2183 AN: 4824

European-Finnish (FIN) AF: 0.414 AC: 4374 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25514 AN: 67972

Other (OTH) AF: 0.430 AC: 908 AN: 2110

Alfa AF: 0.401 Hom.: 6225

Bravo AF: 0.479

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.26
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs236155; hg19: chr20-5905550; COSMIC: COSV66761479; COSMIC: COSV66761479;