Genetic Variant ZNF320:p.Ala398Ala (chr19-52880932-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001351774.2(ZNF320):c.1194G>A(p.Ala398Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 1,613,686 control chromosomes in the GnomAD database, including 374,867 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 0.66 ( 33412 hom., cov: 32)

Exomes 𝑓: 0.68 ( 341455 hom. )

Consequence

ZNF320
NM_001351774.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.60

Publications

32 publications found

Variant links:

Genes affected

ZNF320 (HGNC:13842): (zinc finger protein 320) ZNF320 encodes a Kruppel-like zinc finger protein. Members of this protein family are involved in activation or repression of transcription.[supplied by OMIM, Jul 2002]

ZNF320 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-3.6 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF320	NM_001351774.2 link	c.1194G>A	p.Ala398Ala	synonymous_variant	Exon 6 of 6	ENST00000682928.1	NP_001338703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF320	ENST00000682928.1 link	c.1194G>A	p.Ala398Ala	synonymous_variant	Exon 6 of 6		NM_001351774.2	ENSP00000506814.1		A2RRD8

Frequencies

GnomAD3 genomes

AF:

0.658

AC:

99905

AN:

151802

Hom.:

33397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.733

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.685

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.590

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.633

GnomAD2 exomes

AF:

0.620

AC:

155639

AN:

251208

AF XY:

0.631

show subpopulations

Gnomad AFR exome

AF:

0.678

Gnomad AMR exome

AF:

0.389

Gnomad ASJ exome

AF:

0.676

Gnomad EAS exome

AF:

0.376

Gnomad FIN exome

AF:

0.708

Gnomad NFE exome

AF:

0.694

Gnomad OTH exome

AF:

0.642

GnomAD4 exome

AF:

0.679

AC:

992680

AN:

1461764

Hom.:

341455

Cov.:

AF XY:

0.679

AC XY:

493402

AN XY:

727182

show subpopulations

African (AFR)

AF:

0.679

AC:

22729

AN:

33480

American (AMR)

AF:

0.408

AC:

18261

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

17720

AN:

26132

East Asian (EAS)

AF:

0.410

AC:

16260

AN:

39694

South Asian (SAS)

AF:

0.634

AC:

54643

AN:

86248

European-Finnish (FIN)

AF:

0.707

AC:

37771

AN:

53414

Middle Eastern (MID)

AF:

0.652

AC:

3759

AN:

5766

European-Non Finnish (NFE)

AF:

0.703

AC:

781577

AN:

1111926

Other (OTH)

AF:

0.662

AC:

39960

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

19938

39876

59814

79752

99690

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19632

39264

58896

78528

98160

<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:

0.658

AC:

99966

AN:

151922

Hom.:

33412

Cov.:

AF XY:

0.651

AC XY:

48325

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.675

AC:

27992

AN:

41460

American (AMR)

AF:

0.512

AC:

7807

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.685

AC:

2379

AN:

3472

East Asian (EAS)

AF:

0.385

AC:

1973

AN:

5130

South Asian (SAS)

AF:

0.630

AC:

3033

AN:

4816

European-Finnish (FIN)

AF:

0.710

AC:

7477

AN:

10528

Middle Eastern (MID)

AF:

0.594

AC:

171

AN:

288

European-Non Finnish (NFE)

AF:

0.694

AC:

47138

AN:

67966

Other (OTH)

AF:

0.629

AC:

1329

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1676

3351

5027

6702

8378

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

800

1600

2400

3200

4000

<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:

0.678

Hom.:

157850

Bravo

AF:

0.640

Asia WGS

AF:

0.552

AC:

1920

AN:

3478

EpiCase

AF:

0.693

EpiControl

AF:

0.693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

8.0

(source)

DANN

Benign

0.50

PhyloP100

-3.6

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over