Genetic Variant ZNF230:c.15+144G>T (chr19-44007237-G-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_006300.4(ZNF230):c.15+144G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 690,608 control chromosomes in the GnomAD database, including 149,235 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 0.62 ( 30019 hom., cov: 32)

Exomes 𝑓: 0.65 ( 119216 hom. )

Consequence

ZNF230
NM_006300.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

31 publications found

Variant links:

Genes affected

ZNF230 (HGNC:13024): (zinc finger protein 230) 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF230 links:

ENSG00000293690 (HGNC:):

ENSG00000293690 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=-1.05).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006300.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF230	NM_006300.4	MANE Select	c.15+144G>T		intron	N/A	NP_006291.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF230	ENST00000429154.7	TSL:1 MANE Select	c.15+144G>T	intron	N/A	ENSP00000409318.1
ZNF230	ENST00000585632.5	TSL:2	c.15+144G>T	intron	N/A	ENSP00000465988.1
ZNF230	ENST00000585491.1	TSL:2	c.15+144G>T	intron	N/A	ENSP00000466541.1

Frequencies

GnomAD3 genomes

AF:

0.617

AC:

93671

AN:

151886

Hom.:

30004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.595

Gnomad AMR

AF:

0.467

Gnomad ASJ

AF:

0.629

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.654

AC:

352397

AN:

538604

Hom.:

119216

AF XY:

0.655

AC XY:

178376

AN XY:

272172

show subpopulations

African (AFR)

AF:

0.500

AC:

6675

AN:

13350

American (AMR)

AF:

0.374

AC:

4974

AN:

13292

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

7546

AN:

12322

East Asian (EAS)

AF:

0.320

AC:

8910

AN:

27808

South Asian (SAS)

AF:

0.627

AC:

15039

AN:

23970

European-Finnish (FIN)

AF:

0.705

AC:

27268

AN:

38690

Middle Eastern (MID)

AF:

0.579

AC:

2082

AN:

3596

European-Non Finnish (NFE)

AF:

0.695

AC:

263373

AN:

378708

Other (OTH)

AF:

0.615

AC:

16530

AN:

26868

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

5360

10720

16081

21441

26801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4778

9556

14334

19112

23890

<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:

0.617

AC:

93727

AN:

152004

Hom.:

30019

Cov.:

AF XY:

0.611

AC XY:

45448

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.526

AC:

21776

AN:

41412

American (AMR)

AF:

0.466

AC:

7117

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

2184

AN:

3470

East Asian (EAS)

AF:

0.315

AC:

1631

AN:

5174

South Asian (SAS)

AF:

0.690

AC:

3333

AN:

4830

European-Finnish (FIN)

AF:

0.710

AC:

7515

AN:

10578

Middle Eastern (MID)

AF:

0.565

AC:

166

AN:

294

European-Non Finnish (NFE)

AF:

0.709

AC:

48195

AN:

67952

Other (OTH)

AF:

0.602

AC:

1270

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1725

3451

5176

6902

8627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.636

Hom.:

11602

Bravo

AF:

0.585

Asia WGS

AF:

0.493

AC:

1718

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.072

(source)

DANN

Benign

0.44

PhyloP100

-1.3

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over