16-29779608-GGTCCGA-G

Position:

• chr16-29779608-GGTCCGA-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4 BP6_Moderate BA1

The NM_152338.4(ZG16):​c.163_168delCGAGTC​(p.Arg55_Val56del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.00328 in 1,536,938 control chromosomes in the GnomAD database, including 149 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0069 (23 hom., cov: 31)
  • Exomes 𝑓: 0.0029 (126 hom.)
• Consequence: ZG16 NM_152338.4 conservative_inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.26

Genes affected

ZG16 (HGNC:30961): (zymogen granule protein 16) Predicted to enable carbohydrate binding activity and peptidoglycan binding activity. Predicted to be involved in protein transport. Predicted to act upstream of or within defense response to Gram-positive bacterium and suppression of symbiont entry into host. Located in Golgi lumen and collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_152338.4.
• BP6: Variant 16-29779608-GGTCCGA-G is Benign according to our data. Variant chr16-29779608-GGTCCGA-G is described in ClinVar as [Benign]. Clinvar id is 771485.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZG16	NM_152338.4	c.163_168delCGAGTC	p.Arg55_Val56del	conservative_inframe_deletion	3/4	ENST00000400752.6	NP_689551.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZG16	ENST00000400752.6	c.163_168delCGAGTC	p.Arg55_Val56del	conservative_inframe_deletion	3/4	1	NM_152338.4	ENSP00000383563.4

Frequencies

GnomAD3 genomes AF: 0.00686 AC: 1042 AN: 151810 Hom.: 21 Cov.: 31

Gnomad AFR AF: 0.00148

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00987

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.0126

GnomAD3 exomes AF: 0.0133 AC: 1921 AN: 144826 Hom.: 72 AF XY: 0.0101 AC XY: 777 AN XY: 77284

Gnomad AFR exome AF: 0.00247

Gnomad AMR exome AF: 0.0716

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00518

Gnomad SAS exome AF: 0.000220

Gnomad FIN exome AF: 0.00100

Gnomad NFE exome AF: 0.000403

Gnomad OTH exome AF: 0.0116

GnomAD4 exome AF: 0.00288 AC: 3985 AN: 1385008 Hom.: 126 AF XY: 0.00257 AC XY: 1759 AN XY: 683428

Gnomad4 AFR exome AF: 0.000950

Gnomad4 AMR exome AF: 0.0725

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0125

Gnomad4 SAS exome AF: 0.000341

Gnomad4 FIN exome AF: 0.00143

Gnomad4 NFE exome AF: 0.000605

Gnomad4 OTH exome AF: 0.00324

GnomAD4 genome AF: 0.00690 AC: 1049 AN: 151930 Hom.: 23 Cov.: 31 AF XY: 0.00796 AC XY: 591 AN XY: 74270

Gnomad4 AFR AF: 0.00147

Gnomad4 AMR AF: 0.0557

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00989

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00189

Gnomad4 NFE AF: 0.000604

Gnomad4 OTH AF: 0.0124

Alfa AF: 0.00269 Hom.: 0

Bravo AF: 0.0106

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 06, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200571875; hg19: chr16-29790929;