Genetic Variant ZNF829:c.319+1530G>A (chr19-36906399-C-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_001037232.4(ZNF829):c.319+1530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,038 control chromosomes in the GnomAD database, including 1,642 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 0.14 ( 1642 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF829
NM_001037232.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

2 publications found

Variant links:

Genes affected

ZNF829 (HGNC:34032): (zinc finger protein 829) Predicted to enable DNA-binding transcription factor 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. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF829 links:

ENSG00000291239 (HGNC:):

ENSG00000291239 links:

ZNF345 (HGNC:16367): (zinc finger protein 345) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF345 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
ZNF829	NM_001037232.4 link	c.319+1530G>A	intron_variant	Intron 5 of 5	ENST00000391711.8	NP_001032309.2
ZNF829	NM_001171979.2 link	c.562+1530G>A	intron_variant	Intron 5 of 5		NP_001165450.1
ZNF829	XM_005258876.4 link	c.319+1530G>A	intron_variant	Intron 5 of 5		XP_005258933.1
ZNF829	XM_011526933.3 link	c.319+1530G>A	intron_variant	Intron 5 of 5		XP_011525235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF829	ENST00000391711.8 link	c.319+1530G>A		intron_variant	Intron 5 of 5	1	NM_001037232.4	ENSP00000429266.1
ENSG00000291239	ENST00000706165.1 link	c.-255-11180C>T		intron_variant	Intron 3 of 11			ENSP00000516244.1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20629

AN:

151920

Hom.:

1637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.0518

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.0819

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.0912

Gnomad OTH

AF:

0.150

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.136

AC:

20657

AN:

152038

Hom.:

1642

Cov.:

AF XY:

0.136

AC XY:

10106

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.214

AC:

8874

AN:

41478

American (AMR)

AF:

0.136

AC:

2080

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

473

AN:

3470

East Asian (EAS)

AF:

0.165

AC:

851

AN:

5170

South Asian (SAS)

AF:

0.185

AC:

892

AN:

4816

European-Finnish (FIN)

AF:

0.0819

AC:

866

AN:

10578

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0913

AC:

6202

AN:

67960

Other (OTH)

AF:

0.150

AC:

316

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

896

1793

2689

3586

4482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.111

Hom.:

1375

Bravo

AF:

0.141

Asia WGS

AF:

0.189

AC:

657

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.7

(source)

DANN

Benign

0.55

PhyloP100

-1.0

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