Variant rs9305035 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

ZNF317 (HGNC:):

ZNF317 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF317	NM_020933.5 linkuse as main transcript	c.1648C>A	p.Arg550Arg	synonymous_variant	7/7	ENST00000247956.11	NP_065984.3	Q96PQ6-1A0A024R7B1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF317	ENST00000247956.11 linkuse as main transcript	c.1648C>A	p.Arg550Arg	synonymous_variant	7/7	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

GnomAD3 exomes

AF:

0.0754

AC:

18804

AN:

249382

Hom.:

790

AF XY:

0.0733

AC XY:

9883

AN XY:

134764

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 SAS exome

AF:

0.0585

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

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.0819

Gnomad4 ASJ exome

AF:

0.0934

Gnomad4 EAS exome

AF:

0.0815

Gnomad4 SAS exome

AF:

0.0589

Gnomad4 FIN exome

AF:

0.0414

Gnomad4 NFE exome

AF:

0.0669

Gnomad4 OTH exome

AF:

0.0792

GnomAD4 genome

AF:

0.0985

AC:

14865

AN:

150936

Hom.:

864

Cov.:

AF XY:

0.0980

AC XY:

7231

AN XY:

73780

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.0960

Gnomad4 ASJ

AF:

0.0874

Gnomad4 EAS

AF:

0.0952

Gnomad4 SAS

AF:

0.0579

Gnomad4 FIN

AF:

0.0389

Gnomad4 NFE

AF:

0.0678

Gnomad4 OTH

AF:

0.0926

Alfa

AF:

0.0685

Hom.:

241

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

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over