Genetic Variant ZNF219:p.Gln233_Pro234dup (chr14-21092593-G-GGAGGCT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_016423.3(ZNF219):c.698_703dupAGCCTC(p.Gln233_Pro234dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000268 in 1,547,654 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., cov: 29)

Exomes 𝑓: 0.00028 ( 0 hom. )

Consequence

ZNF219
NM_016423.3 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.447

Publications

9 publications found

Variant links:

Genes affected

ZNF219 (HGNC:13011): (zinc finger protein 219) This gene is a member of the Kruppel-like zinc finger gene family. The encoded protein functions as a transcriptional repressor of the high mobility group nucleosome binding domain 1 protein, which is associated with transcriptionally active chromatin. [provided by RefSeq, Apr 2017]

ZNF219 Gene-Disease associations (from GenCC):

microphthalmia
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ZNF219 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
ZNF219	NM_016423.3 link	c.698_703dupAGCCTC	p.Gln233_Pro234dup	conservative_inframe_insertion	Exon 3 of 5	ENST00000360947.8	NP_057507.2
ZNF219	NM_001101672.2 link	c.698_703dupAGCCTC	p.Gln233_Pro234dup	conservative_inframe_insertion	Exon 3 of 5		NP_001095142.1
ZNF219	NM_001102454.2 link	c.698_703dupAGCCTC	p.Gln233_Pro234dup	conservative_inframe_insertion	Exon 3 of 5		NP_001095924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
ZNF219	ENST00000360947.8 link	c.698_703dupAGCCTC	p.Gln233_Pro234dup	conservative_inframe_insertion	Exon 3 of 5	1	NM_016423.3	ENSP00000354206.3
ZNF219	ENST00000421093.6 link	c.698_703dupAGCCTC	p.Gln233_Pro234dup	conservative_inframe_insertion	Exon 3 of 5	1		ENSP00000392401.2
ZNF219	ENST00000451119.6 link	c.698_703dupAGCCTC	p.Gln233_Pro234dup	conservative_inframe_insertion	Exon 3 of 5	5		ENSP00000388558.2
ZNF219	ENST00000555270.5 link	c.64_69dupAGCCTC		downstream_gene_variant		4		ENSP00000450803.1

Frequencies

GnomAD3 genomes

AF:

0.000171

AC:

AN:

151776

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000969

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000969

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.000481

GnomAD2 exomes

AF:

0.000240

AC:

AN:

145600

AF XY:

0.000255

show subpopulations

Gnomad AFR exome

AF:

0.000136

Gnomad AMR exome

AF:

0.000163

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000882

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000307

Gnomad OTH exome

AF:

0.000477

GnomAD4 exome

AF:

0.000278

AC:

388

AN:

1395758

Hom.:

Cov.:

AF XY:

0.000269

AC XY:

185

AN XY:

688732

show subpopulations

African (AFR)

AF:

0.000156

AC:

AN:

31956

American (AMR)

AF:

0.000140

AC:

AN:

35760

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25168

East Asian (EAS)

AF:

0.000496

AC:

AN:

36320

South Asian (SAS)

AF:

0.0000756

AC:

AN:

79398

European-Finnish (FIN)

AF:

0.0000458

AC:

AN:

43712

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5392

European-Non Finnish (NFE)

AF:

0.000305

AC:

329

AN:

1080032

Other (OTH)

AF:

0.000396

AC:

AN:

58020

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

102

128

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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:

0.000171

AC:

AN:

151896

Hom.:

Cov.:

AF XY:

0.000215

AC XY:

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.0000966

AC:

AN:

41400

American (AMR)

AF:

0.000131

AC:

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.000972

AC:

AN:

5146

South Asian (SAS)

AF:

0.00

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.0000943

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000191

AC:

AN:

67898

Other (OTH)

AF:

0.000476

AC:

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.0000451

Hom.:

247

Bravo

AF:

0.000170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.45

Mutation Taster

=77/23

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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14-21092593-GGAGGCTGAGGCT-GGAGGCTGAGGCTGAGGCT

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