Genetic Variant ENSG00000296363:n.145-959C>G (chr19-22286431-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000738586.1(ENSG00000296363):n.145-959C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,466,980 control chromosomes in the GnomAD database, including 165,144 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 0.47 ( 16209 hom., cov: 22)

Exomes 𝑓: 0.47 ( 148935 hom. )

Consequence

ENSG00000296363
ENST00000738586.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.687

Publications

5 publications found

Variant links:

Genes affected

ENSG00000296363 (HGNC:):

ENSG00000296363 links:

ZNF729 (HGNC:32464): (zinc finger protein 729) Predicted to enable DNA-binding transcription activator 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 active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF729 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF729	NM_001242680.2 link	c.-95G>C		upstream_gene_variant		ENST00000601693.2	NP_001229609.1	A6NN14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296363	ENST00000738586.1 link	n.145-959C>G		intron_variant	Intron 1 of 1
ZNF729	ENST00000601693.2 link	c.-95G>C		upstream_gene_variant		2	NM_001242680.2	ENSP00000469582.1		A6NN14

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

68161

AN:

146288

Hom.:

16204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.590

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.469

Gnomad MID

AF:

0.390

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.453

GnomAD4 exome

AF:

0.469

AC:

619158

AN:

1320576

Hom.:

148935

Cov.:

AF XY:

0.462

AC XY:

303642

AN XY:

657900

show subpopulations

African (AFR)

AF:

0.476

AC:

14220

AN:

29844

American (AMR)

AF:

0.467

AC:

17061

AN:

36558

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

9092

AN:

24592

East Asian (EAS)

AF:

0.259

AC:

9217

AN:

35576

South Asian (SAS)

AF:

0.258

AC:

20657

AN:

79912

European-Finnish (FIN)

AF:

0.473

AC:

19067

AN:

40340

Middle Eastern (MID)

AF:

0.338

AC:

1865

AN:

5524

European-Non Finnish (NFE)

AF:

0.497

AC:

503140

AN:

1012592

Other (OTH)

AF:

0.446

AC:

24839

AN:

55638

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

15944

31889

47833

63778

79722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14358

28716

43074

57432

71790

<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:

0.466

AC:

68189

AN:

146404

Hom.:

16209

Cov.:

AF XY:

0.459

AC XY:

32615

AN XY:

71032

show subpopulations

African (AFR)

AF:

0.479

AC:

18948

AN:

39548

American (AMR)

AF:

0.457

AC:

6607

AN:

14458

Ashkenazi Jewish (ASJ)

AF:

0.367

AC:

1258

AN:

3430

East Asian (EAS)

AF:

0.296

AC:

1445

AN:

4882

South Asian (SAS)

AF:

0.240

AC:

1036

AN:

4324

European-Finnish (FIN)

AF:

0.469

AC:

4698

AN:

10008

Middle Eastern (MID)

AF:

0.375

AC:

108

AN:

288

European-Non Finnish (NFE)

AF:

0.491

AC:

32672

AN:

66588

Other (OTH)

AF:

0.449

AC:

897

AN:

1996

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1695

3390

5086

6781

8476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

606

1212

1818

2424

3030

<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:

0.480

Hom.:

2203

Bravo

AF:

0.473

Asia WGS

AF:

0.259

AC:

901

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.66

(source)

DANN

Benign

0.43

PhyloP100

-0.69

PromoterAI

0.0068

Neutral

(source)

Mutation Taster

=299/1

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over