Genetic Variant ZBTB17:c.1070+36G>T (chr1-15944661-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003443.3(ZBTB17):c.1070+36G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 1,602,604 control chromosomes in the GnomAD database, including 5,878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.098 ( 965 hom., cov: 33)

Exomes 𝑓: 0.078 ( 4913 hom. )

Consequence

ZBTB17
NM_003443.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.590

Publications

3 publications found

Variant links:

Genes affected

ZBTB17 (HGNC:12936): (zinc finger and BTB domain containing 17) This gene encodes a zinc finger protein involved in the regulation of c-myc. The symbol MIZ1 has also been associated with PIAS2 which is a different gene located on chromosome 18. [provided by RefSeq, Jul 2008]

ZBTB17 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 1-15944661-C-A is Benign according to our data. Variant chr1-15944661-C-A is described in ClinVar as Benign. ClinVar VariationId is 1258996.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB17	NM_003443.3 link	c.1070+36G>T		intron_variant	Intron 8 of 15	ENST00000375743.9	NP_003434.2	Q13105-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB17	ENST00000375743.9 link	c.1070+36G>T		intron_variant	Intron 8 of 15	1	NM_003443.3	ENSP00000364895.4		Q13105-1

Frequencies

GnomAD3 genomes

AF:

0.0977

AC:

14861

AN:

152140

Hom.:

965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.0553

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0924

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0748

Gnomad OTH

AF:

0.0583

GnomAD2 exomes

AF:

0.0673

AC:

15970

AN:

237272

AF XY:

0.0661

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.0339

Gnomad ASJ exome

AF:

0.0932

Gnomad EAS exome

AF:

0.000165

Gnomad FIN exome

AF:

0.0990

Gnomad NFE exome

AF:

0.0761

Gnomad OTH exome

AF:

0.0706

GnomAD4 exome

AF:

0.0781

AC:

113217

AN:

1450346

Hom.:

4913

Cov.:

AF XY:

0.0764

AC XY:

55136

AN XY:

722052

show subpopulations

African (AFR)

AF:

0.181

AC:

6066

AN:

33462

American (AMR)

AF:

0.0370

AC:

1655

AN:

44678

Ashkenazi Jewish (ASJ)

AF:

0.0970

AC:

2532

AN:

26100

East Asian (EAS)

AF:

0.000328

AC:

AN:

39686

South Asian (SAS)

AF:

0.0338

AC:

2915

AN:

86212

European-Finnish (FIN)

AF:

0.0958

AC:

4097

AN:

42760

Middle Eastern (MID)

AF:

0.0498

AC:

279

AN:

5602

European-Non Finnish (NFE)

AF:

0.0820

AC:

91183

AN:

1111596

Other (OTH)

AF:

0.0743

AC:

4477

AN:

60250

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

7242

14484

21726

28968

36210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3482

6964

10446

13928

17410

<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:

0.0977

AC:

14873

AN:

152258

Hom.:

965

Cov.:

AF XY:

0.0961

AC XY:

7154

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.175

AC:

7267

AN:

41540

American (AMR)

AF:

0.0552

AC:

844

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

370

AN:

3472

East Asian (EAS)

AF:

0.000386

AC:

AN:

5178

South Asian (SAS)

AF:

0.0263

AC:

127

AN:

4826

European-Finnish (FIN)

AF:

0.0924

AC:

980

AN:

10608

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0748

AC:

5089

AN:

68018

Other (OTH)

AF:

0.0572

AC:

121

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

646

1292

1939

2585

3231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0842

Hom.:

Bravo

AF:

0.0989

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 16, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.56

(source)

DANN

Benign

0.78

PhyloP100

-0.59

PromoterAI

-0.0072

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over