Genetic Variant ZNF317:p.Arg550Arg (chr19-9161293-C-A) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_020933.5(ZNF317):c.1648C>A(p.Arg550Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 1,603,104 control chromosomes in the GnomAD database, including 4,812 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 0.098 ( 864 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3948 hom. )

Consequence

ZNF317
NM_020933.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

7 publications found

Variant links:

Genes affected

ZNF317 (HGNC:13507): (zinc finger protein 317) 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. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF317 links:

Genome browser will be placed here

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=-0.51).

BP7

Synonymous conserved (PhyloP=-1.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF317	NM_020933.5 link	c.1648C>A	p.Arg550Arg	synonymous_variant	Exon 7 of 7	ENST00000247956.11	NP_065984.3	Q96PQ6-1A0A024R7B1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF317	ENST00000247956.11 link	c.1648C>A	p.Arg550Arg	synonymous_variant	Exon 7 of 7	1	NM_020933.5	ENSP00000247956.5		Q96PQ6-1

Frequencies

GnomAD3 genomes

AF:

0.0982

AC:

14812

AN:

150814

Hom.:

854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.0964

Gnomad ASJ

AF:

0.0874

Gnomad EAS

AF:

0.0948

Gnomad SAS

AF:

0.0583

Gnomad FIN

AF:

0.0389

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0678

Gnomad OTH

AF:

0.0899

GnomAD2 exomes

AF:

0.0754

AC:

18804

AN:

249382

AF XY:

0.0733

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.0761

Gnomad ASJ exome

AF:

0.0947

Gnomad EAS exome

AF:

0.105

Gnomad FIN exome

AF:

0.0400

Gnomad NFE exome

AF:

0.0672

Gnomad OTH exome

AF:

0.0765

GnomAD4 exome

AF:

0.0699

AC:

101579

AN:

1452168

Hom.:

3948

Cov.:

AF XY:

0.0694

AC XY:

50135

AN XY:

722044

show subpopulations

African (AFR)

AF:

0.172

AC:

5744

AN:

33328

American (AMR)

AF:

0.0819

AC:

3484

AN:

42556

Ashkenazi Jewish (ASJ)

AF:

0.0934

AC:

2431

AN:

26014

East Asian (EAS)

AF:

0.0815

AC:

3199

AN:

39246

South Asian (SAS)

AF:

0.0589

AC:

4954

AN:

84172

European-Finnish (FIN)

AF:

0.0414

AC:

2209

AN:

53318

Middle Eastern (MID)

AF:

0.115

AC:

661

AN:

5754

European-Non Finnish (NFE)

AF:

0.0669

AC:

74136

AN:

1107696

Other (OTH)

AF:

0.0792

AC:

4761

AN:

60084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

6231

12462

18693

24924

31155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2872

5744

8616

11488

14360

<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:

0.0985

AC:

14865

AN:

150936

Hom.:

864

Cov.:

AF XY:

0.0980

AC XY:

7231

AN XY:

73780

show subpopulations

African (AFR)

AF:

0.169

AC:

6966

AN:

41114

American (AMR)

AF:

0.0960

AC:

1459

AN:

15202

Ashkenazi Jewish (ASJ)

AF:

0.0874

AC:

302

AN:

3454

East Asian (EAS)

AF:

0.0952

AC:

477

AN:

5010

South Asian (SAS)

AF:

0.0579

AC:

276

AN:

4766

European-Finnish (FIN)

AF:

0.0389

AC:

411

AN:

10554

Middle Eastern (MID)

AF:

0.150

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.0678

AC:

4583

AN:

67548

Other (OTH)

AF:

0.0926

AC:

194

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

680

1359

2039

2718

3398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0694

Hom.:

254

Bravo

AF:

0.105

Asia WGS

AF:

0.0720

AC:

249

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

6.4

(source)

DANN

Benign

0.65

PhyloP100

-1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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