dbSNP rs3752120: ZNF432:c.-266G>A (chr19-52048768-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_014650.4(ZNF432):c.-266G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,718 control chromosomes in the GnomAD database, including 2,181 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 0.15 ( 2174 hom., cov: 31)

Exomes 𝑓: 0.13 ( 7 hom. )

Consequence

ZNF432
NM_014650.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.492

Publications

32 publications found

Variant links:

Genes affected

ZNF432 (HGNC:20810): (zinc finger protein 432) 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. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF432 links:

ENSG00000275055 (HGNC:):

ENSG00000275055 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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ZNF432	NM_014650.4 link	c.-266G>A	5_prime_UTR_variant	Exon 1 of 5	ENST00000221315.10	NP_055465.1	O94892A0A024R4I3
ZNF432	NM_001322284.2 link	c.-352G>A	upstream_gene_variant			NP_001309213.1	O94892A0A024R4I3
ZNF432	NM_001322285.1 link	c.-420G>A	upstream_gene_variant			NP_001309214.1	O94892A0A024R4I3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF432	ENST00000221315.10 link	c.-266G>A		5_prime_UTR_variant	Exon 1 of 5	1	NM_014650.4	ENSP00000221315.4		O94892

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22325

AN:

152064

Hom.:

2171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0532

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.169

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.156

GnomAD4 exome

AF:

0.134

AC:

AN:

536

Hom.:

Cov.:

AF XY:

0.115

AC XY:

AN XY:

340

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.157

AC:

AN:

236

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.100

AC:

AN:

250

Other (OTH)

AF:

0.154

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.147

AC:

22352

AN:

152182

Hom.:

2174

Cov.:

AF XY:

0.152

AC XY:

11290

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0532

AC:

2208

AN:

41538

American (AMR)

AF:

0.192

AC:

2932

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

402

AN:

3468

East Asian (EAS)

AF:

0.377

AC:

1946

AN:

5156

South Asian (SAS)

AF:

0.287

AC:

1388

AN:

4828

European-Finnish (FIN)

AF:

0.165

AC:

1747

AN:

10580

Middle Eastern (MID)

AF:

0.164

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.165

AC:

11225

AN:

67998

Other (OTH)

AF:

0.158

AC:

334

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

938

1876

2813

3751

4689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.160

Hom.:

6222

Bravo

AF:

0.144

Asia WGS

AF:

0.322

AC:

1117

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.5

(source)

DANN

Benign

0.76

PhyloP100

-0.49

PromoterAI

0.056

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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