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

Variant summary

Our verdict is Benign. The variant received -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

Publications

18 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

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.*37G>T		3_prime_UTR	Exon 4 of 4	NP_660295.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZG16B	ENST00000382280.8	TSL:1 MANE Select	c.*37G>T	3_prime_UTR	Exon 4 of 4	ENSP00000371715.4
ZG16B	ENST00000572863.2	TSL:2	c.*37G>T	3_prime_UTR	Exon 3 of 3	ENSP00000461740.2
ZG16B	ENST00000570670.6	TSL:3	c.155+1400G>T	intron	N/A	ENSP00000460793.2

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

GnomAD2 exomes

AF:

0.662

AC:

157464

AN:

237700

AF XY:

0.669

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 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

African (AFR)

AF:

0.504

AC:

16617

AN:

32958

American (AMR)

AF:

0.603

AC:

26229

AN:

43486

Ashkenazi Jewish (ASJ)

AF:

0.731

AC:

18127

AN:

24784

East Asian (EAS)

AF:

0.626

AC:

24649

AN:

39348

South Asian (SAS)

AF:

0.704

AC:

58964

AN:

83732

European-Finnish (FIN)

AF:

0.639

AC:

33470

AN:

52342

Middle Eastern (MID)

AF:

0.724

AC:

3401

AN:

4698

European-Non Finnish (NFE)

AF:

0.688

AC:

755233

AN:

1097576

Other (OTH)

AF:

0.688

AC:

40764

AN:

59292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

17119

34239

51358

68478

85597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19424

38848

58272

77696

97120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.633

AC:

96132

AN:

151958

Hom.:

30900

Cov.:

AF XY:

0.630

AC XY:

46771

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.512

AC:

21191

AN:

41396

American (AMR)

AF:

0.642

AC:

9813

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.740

AC:

2566

AN:

3468

East Asian (EAS)

AF:

0.674

AC:

3483

AN:

5166

South Asian (SAS)

AF:

0.691

AC:

3326

AN:

4816

European-Finnish (FIN)

AF:

0.629

AC:

6641

AN:

10564

Middle Eastern (MID)

AF:

0.701

AC:

206

AN:

294

European-Non Finnish (NFE)

AF:

0.689

AC:

46850

AN:

67948

Other (OTH)

AF:

0.666

AC:

1408

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1786

3571

5357

7142

8928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.669

Hom.:

94429

Bravo

AF:

0.625

Asia WGS

AF:

0.648

AC:

2254

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.60

(source)

DANN

Benign

0.55

PhyloP100

-0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over