dbSNP rs624903: ZBTB34:c.*4029C>T (chr9-126884943-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001099270.4(ZBTB34):c.*4029C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.105 in 166,966 control chromosomes in the GnomAD database, including 1,036 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 0.11 ( 1011 hom., cov: 32)

Exomes 𝑓: 0.063 ( 25 hom. )

Consequence

ZBTB34
NM_001099270.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.49

Publications

4 publications found

Variant links:

Genes affected

ZBTB34 (HGNC:31446): (zinc finger and BTB domain containing 34) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB34 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ZBTB34	NM_001099270.4 link	c.*4029C>T	3_prime_UTR_variant	Exon 2 of 2	ENST00000319119.5	NP_001092740.2	Q8NCN2
ZBTB34	NM_001395198.1 link	c.*4029C>T	3_prime_UTR_variant	Exon 3 of 3		NP_001382127.1
ZBTB34	XM_047423402.1 link	c.*4029C>T	3_prime_UTR_variant	Exon 3 of 3		XP_047279358.1
ZBTB34	XM_011518699.4 link	c.*4029C>T	3_prime_UTR_variant	Exon 2 of 2		XP_011517001.1	Q8NCN2A0A0C4DFQ2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB34	ENST00000319119.5 link	c.*4029C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001099270.4	ENSP00000317534.4		A0A0C4DFQ2
ZBTB34	ENST00000695642.1 link	c.*4029C>T		3_prime_UTR_variant	Exon 3 of 3			ENSP00000512077.1		A0A8Q3WKM1

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16568

AN:

151978

Hom.:

1005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.00673

Gnomad SAS

AF:

0.0275

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.121

GnomAD4 exome

AF:

0.0629

AC:

935

AN:

14870

Hom.:

Cov.:

AF XY:

0.0629

AC XY:

444

AN XY:

7058

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0625

AC:

918

AN:

14684

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.110

AC:

AN:

Other (OTH)

AF:

0.0778

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

138

184

230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.109

AC:

16590

AN:

152096

Hom.:

1011

Cov.:

AF XY:

0.106

AC XY:

7900

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.116

AC:

4809

AN:

41464

American (AMR)

AF:

0.123

AC:

1886

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

448

AN:

3468

East Asian (EAS)

AF:

0.00694

AC:

AN:

5186

South Asian (SAS)

AF:

0.0282

AC:

136

AN:

4826

European-Finnish (FIN)

AF:

0.0665

AC:

704

AN:

10588

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8183

AN:

67978

Other (OTH)

AF:

0.120

AC:

253

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

729

1458

2187

2916

3645

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.114

Hom.:

355

Bravo

AF:

0.116

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

6.5

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over