rs9925556

Variant names:

• chr16-2830104-C-G
• rs9925556
• NM_145252.3:c.-252C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-2830104-C-G
• chr16-2830104-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145252.3(ZG16B):​c.-252C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZG16B NM_145252.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687
• Publications: 24 publications found

Genes affected

ZG16B (HGNC:30456): (zymogen granule protein 16B) Predicted to enable carbohydrate binding activity. Involved in retina homeostasis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145252.3. 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
	ZG16B	NM_145252.3	MANE Select	c.-252C>G		upstream_gene	N/A	NP_660295.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZG16B	ENST00000382280.8	TSL:1 MANE Select	c.-252C>G		upstream_gene	N/A	ENSP00000371715.4
	ZG16B	ENST00000570670.6	TSL:3	c.-252C>G		upstream_gene	N/A	ENSP00000460793.2
	ZG16B	ENST00000571723.2	TSL:2	c.-252C>G		upstream_gene	N/A	ENSP00000458847.2

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 492606 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 255012

African (AFR) AF: 0.00 AC: 0 AN: 12206

American (AMR) AF: 0.00 AC: 0 AN: 15800

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13490

East Asian (EAS) AF: 0.00 AC: 0 AN: 29100

South Asian (SAS) AF: 0.00 AC: 0 AN: 42356

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41898

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2018

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 308910

Other (OTH) AF: 0.00 AC: 0 AN: 26828

GnomAD4 genome Cov.: 35

Alfa AF: 0.00 Hom.: 44301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		0.69
PromoterAI		-0.00080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9925556; hg19: chr16-2880105;