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:

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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=-0.51).

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020933.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF317	NM_020933.5	MANE Select	c.1648C>A	p.Arg550Arg	synonymous	Exon 7 of 7	NP_065984.3
ZNF317	NM_001190791.2		c.1552C>A	p.Arg518Arg	synonymous	Exon 6 of 6	NP_001177720.1	Q96PQ6-2
ZNF317	NR_102435.2		n.2082C>A		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF317	ENST00000247956.11	TSL:1 MANE Select	c.1648C>A	p.Arg550Arg	synonymous	Exon 7 of 7	ENSP00000247956.5	Q96PQ6-1
ZNF317	ENST00000360385.7	TSL:1	c.1552C>A	p.Arg518Arg	synonymous	Exon 6 of 6	ENSP00000353554.2	Q96PQ6-2
ZNF317	ENST00000591278.5	TSL:1	n.*1473C>A		non_coding_transcript_exon	Exon 7 of 7	ENSP00000465780.1	K7EKT9

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over