dbSNP rs4802207: ZNF224:c.-157-119C>T (chr19-44096224-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_001321645.3(ZNF224):c.-157-119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,986 control chromosomes in the GnomAD database, including 34,635 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 0.64 ( 34635 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

ZNF224
NM_001321645.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.461

Publications

13 publications found

Variant links:

Genes affected

ZNF224 (HGNC:13017): (zinc finger protein 224) This gene encodes a member of the Krueppel C2H2-type zinc-finger family of proteins. The encoded protein represses transcription of the aldolase A gene, which encodes a key enzyme in glycolysis. The encoded zinc-finger protein may also function as a transcriptional co-activator with Wilms' tumor protein 1 to regulate apoptotic genes in leukemia. [provided by RefSeq, Jul 2016]

ZNF224 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321645.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF224	NM_001321645.3	MANE Select	c.-157-119C>T		intron	N/A	NP_001308574.1	Q9NZL3
	ZNF224	NM_013398.5		c.-157-119C>T		intron	N/A	NP_037530.2	Q9NZL3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF224	ENST00000693561.1	MANE Select	c.-157-119C>T	intron	N/A	ENSP00000508532.1	Q9NZL3
ZNF224	ENST00000336976.10	TSL:1	c.-157-119C>T	intron	N/A	ENSP00000337368.5	Q9NZL3
ZNF224	ENST00000589870.5	TSL:3	c.-276C>T	5_prime_UTR	Exon 1 of 4	ENSP00000465886.1	K7EL24

Frequencies

GnomAD3 genomes

AF:

0.639

AC:

97044

AN:

151868

Hom.:

34633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.724

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.775

Gnomad EAS

AF:

0.540

Gnomad SAS

AF:

0.680

Gnomad FIN

AF:

0.742

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.826

Gnomad OTH

AF:

0.690

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

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)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.639

AC:

97048

AN:

151986

Hom.:

34635

Cov.:

AF XY:

0.631

AC XY:

46892

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.328

AC:

13565

AN:

41414

American (AMR)

AF:

0.549

AC:

8382

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.775

AC:

2686

AN:

3468

East Asian (EAS)

AF:

0.540

AC:

2795

AN:

5174

South Asian (SAS)

AF:

0.682

AC:

3288

AN:

4820

European-Finnish (FIN)

AF:

0.742

AC:

7813

AN:

10526

Middle Eastern (MID)

AF:

0.745

AC:

219

AN:

294

European-Non Finnish (NFE)

AF:

0.826

AC:

56187

AN:

67988

Other (OTH)

AF:

0.688

AC:

1453

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1447

2893

4340

5786

7233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.768

Hom.:

136242

Bravo

AF:

0.610

Asia WGS

AF:

0.577

AC:

2004

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.95

(source)

DANN

Benign

0.62

PhyloP100

-0.46

PromoterAI

0.0029

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over