16-2830104-C-T

Variant names:

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

Variant summary

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

The NM_145252.3(ZG16B):​c.-252C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 644,222 control chromosomes in the GnomAD database, including 154,467 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 0.71 (38617 hom., cov: 35)
  • Exomes 𝑓: 0.68 (115850 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZG16B	NM_145252.3	MANE Select	c.-252C>T		upstream_gene	N/A	NP_660295.3	Q96DA0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZG16B	ENST00000382280.8	TSL:1 MANE Select	c.-252C>T		upstream_gene	N/A	ENSP00000371715.4	Q96DA0
	ZG16B	ENST00000902257.1		c.-230C>T		upstream_gene	N/A	ENSP00000572316.1
	ZG16B	ENST00000570670.6	TSL:3	c.-252C>T		upstream_gene	N/A	ENSP00000460793.2	I3L3X0

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107999 AN: 152082 Hom.: 38591 Cov.: 35

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.729

GnomAD4 exome AF: 0.685 AC: 336909 AN: 492022 Hom.: 115850 AF XY: 0.686 AC XY: 174832 AN XY: 254712

African (AFR) AF: 0.776 AC: 9471 AN: 12200

American (AMR) AF: 0.643 AC: 10145 AN: 15788

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 9809 AN: 13474

East Asian (EAS) AF: 0.607 AC: 17653 AN: 29080

South Asian (SAS) AF: 0.704 AC: 29785 AN: 42280

European-Finnish (FIN) AF: 0.641 AC: 26832 AN: 41832

Middle Eastern (MID) AF: 0.758 AC: 1528 AN: 2016

European-Non Finnish (NFE) AF: 0.690 AC: 212944 AN: 308556

Other (OTH) AF: 0.699 AC: 18742 AN: 26796

GnomAD4 genome AF: 0.710 AC: 108081 AN: 152200 Hom.: 38617 Cov.: 35 AF XY: 0.705 AC XY: 52442 AN XY: 74424

African (AFR) AF: 0.783 AC: 32537 AN: 41532

American (AMR) AF: 0.669 AC: 10235 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2569 AN: 3470

East Asian (EAS) AF: 0.668 AC: 3443 AN: 5154

South Asian (SAS) AF: 0.691 AC: 3339 AN: 4832

European-Finnish (FIN) AF: 0.628 AC: 6668 AN: 10612

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46888 AN: 67984

Other (OTH) AF: 0.728 AC: 1538 AN: 2114

Alfa AF: 0.694 Hom.: 44301

Bravo AF: 0.713

Asia WGS AF: 0.664 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		0.69
PromoterAI		0.56	Over-expression
Mutation Taster		=100/0	polymorphism

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;