Variant 19-44107267-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001321645.3(ZNF224):c.1107A>G(p.Glu369=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 1,582,610 control chromosomes in the GnomAD database, including 505,767 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 0.74 ( 42217 hom., cov: 32)

Exomes 𝑓: 0.80 ( 463550 hom. )

Consequence

ZNF224
NM_001321645.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.499

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:

ZNF225-AS1 (HGNC:55916): (ZNF225 and ZNF224 antisense RNA 1)

ZNF225-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=-0.499 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ZNF224	NM_001321645.3 linkuse as main transcript	c.1107A>G	p.Glu369=	synonymous_variant	6/6	ENST00000693561.1
ZNF225-AS1	NR_033341.1 linkuse as main transcript	n.1433T>C		non_coding_transcript_exon_variant	2/2
ZNF224	NM_013398.5 linkuse as main transcript	c.1107A>G	p.Glu369=	synonymous_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF224	ENST00000693561.1 linkuse as main transcript	c.1107A>G	p.Glu369=	synonymous_variant	6/6		NM_001321645.3	P1
ZNF225-AS1	ENST00000661725.1 linkuse as main transcript	n.1433T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.738

AC:

112122

AN:

151950

Hom.:

42190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.666

Gnomad AMI

AF:

0.722

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.800

Gnomad EAS

AF:

0.548

Gnomad SAS

AF:

0.680

Gnomad FIN

AF:

0.740

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.759

GnomAD3 exomes

AF:

0.721

AC:

161962

AN:

224612

Hom.:

60413

AF XY:

0.731

AC XY:

88293

AN XY:

120754

show subpopulations

Gnomad AFR exome

AF:

0.660

Gnomad AMR exome

AF:

0.493

Gnomad ASJ exome

AF:

0.795

Gnomad EAS exome

AF:

0.544

Gnomad SAS exome

AF:

0.684

Gnomad FIN exome

AF:

0.746

Gnomad NFE exome

AF:

0.825

Gnomad OTH exome

AF:

0.757

GnomAD4 exome

AF:

0.800

AC:

1144390

AN:

1430542

Hom.:

463550

Cov.:

AF XY:

0.799

AC XY:

566429

AN XY:

709310

show subpopulations

Gnomad4 AFR exome

AF:

0.655

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.793

Gnomad4 EAS exome

AF:

0.540

Gnomad4 SAS exome

AF:

0.688

Gnomad4 FIN exome

AF:

0.744

Gnomad4 NFE exome

AF:

0.837

Gnomad4 OTH exome

AF:

0.777

GnomAD4 genome

AF:

0.738

AC:

112189

AN:

152068

Hom.:

42217

Cov.:

AF XY:

0.727

AC XY:

53997

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.666

Gnomad4 AMR

AF:

0.590

Gnomad4 ASJ

AF:

0.800

Gnomad4 EAS

AF:

0.548

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.740

Gnomad4 NFE

AF:

0.829

Gnomad4 OTH

AF:

0.756

Alfa

AF:

0.804

Hom.:

68901

Bravo

AF:

0.723

Asia WGS

AF:

0.600

AC:

2090

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

9.2

DANN

Benign

0.50

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over