1-15944661-C-A

Variant names:

• chr1-15944661-C-A
• rs12134932
• NM_003443.3:c.1070+36G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.590
• Publications: 3 publications found

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]

ACMG classification

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	c.1070+36G>T		intron_variant	Intron 8 of 15	ENST00000375743.9	NP_003434.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14861 AN: 152140 Hom.: 965 Cov.: 33

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

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.: 32 AF XY: 0.0764 AC XY: 55136 AN XY: 722052

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: 13 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

GnomAD4 genome AF: 0.0977 AC: 14873 AN: 152258 Hom.: 965 Cov.: 33 AF XY: 0.0961 AC XY: 7154 AN XY: 74436

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: 2 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: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5089 AN: 68018

Other (OTH) AF: 0.0572 AC: 121 AN: 2116

Alfa AF: 0.0842 Hom.: 85

Bravo AF: 0.0989

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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
DANN	Benign	0.78
PhyloP100		-0.59
PromoterAI		-0.0072	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12134932; hg19: chr1-16271156;