Genetic Variant ZG16B:c.*37G>T (chr16-2832196-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145252.3(ZG16B):c.*37G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 1,590,174 control chromosomes in the GnomAD database, including 364,064 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 0.63 ( 30900 hom., cov: 31)

Exomes 𝑓: 0.68 ( 333164 hom. )

Consequence

ZG16B
NM_145252.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.448

Variant links:

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]

ZG16B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZG16B	NM_145252.3 link	c.*37G>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000382280.8	NP_660295.3	Q96DA0G8H6I3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZG16B	ENST00000382280.8 link	c.*37G>T	3_prime_UTR_variant	Exon 4 of 4	1	NM_145252.3	ENSP00000371715.4	Q96DA0
ZG16B	ENST00000572863.2 link	c.*37G>T	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000461740.2	A0A0C4DGN4
ZG16B	ENST00000570670.6 link	c.155+1400G>T	intron_variant	Intron 3 of 3	3		ENSP00000460793.2	I3L3X0
ZG16B	ENST00000573019.1 link	n.*221G>T	downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

96069

AN:

151840

Hom.:

30882

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.712

Gnomad AMR

AF:

0.641

Gnomad ASJ

AF:

0.740

Gnomad EAS

AF:

0.674

Gnomad SAS

AF:

0.690

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.667

GnomAD3 exomes

AF:

0.662

AC:

157464

AN:

237700

Hom.:

52699

AF XY:

0.669

AC XY:

86120

AN XY:

128652

show subpopulations

Gnomad AFR exome

AF:

0.506

Gnomad AMR exome

AF:

0.598

Gnomad ASJ exome

AF:

0.729

Gnomad EAS exome

AF:

0.685

Gnomad SAS exome

AF:

0.701

Gnomad FIN exome

AF:

0.635

Gnomad NFE exome

AF:

0.689

Gnomad OTH exome

AF:

0.689

GnomAD4 exome

AF:

0.680

AC:

977454

AN:

1438216

Hom.:

333164

Cov.:

AF XY:

0.682

AC XY:

485555

AN XY:

712198

show subpopulations

Gnomad4 AFR exome

AF:

0.504

Gnomad4 AMR exome

AF:

0.603

Gnomad4 ASJ exome

AF:

0.731

Gnomad4 EAS exome

AF:

0.626

Gnomad4 SAS exome

AF:

0.704

Gnomad4 FIN exome

AF:

0.639

Gnomad4 NFE exome

AF:

0.688

Gnomad4 OTH exome

AF:

0.688

GnomAD4 genome

AF:

0.633

AC:

96132

AN:

151958

Hom.:

30900

Cov.:

AF XY:

0.630

AC XY:

46771

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.512

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.740

Gnomad4 EAS

AF:

0.674

Gnomad4 SAS

AF:

0.691

Gnomad4 FIN

AF:

0.629

Gnomad4 NFE

AF:

0.689

Gnomad4 OTH

AF:

0.666

Alfa

AF:

0.683

Hom.:

60722

Bravo

AF:

0.625

Asia WGS

AF:

0.648

AC:

2254

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.60

DANN

Benign

0.55

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over