Variant rs1404453 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015852.5(ZNF117):c.1282C>T(p.Arg428*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 1,612,614 control chromosomes in the GnomAD database, including 713,237 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 0.90 ( 61559 hom., cov: 30)

Exomes 𝑓: 0.94 ( 651678 hom. )

Consequence

ZNF117
NM_015852.5 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.90

Variant links:

Genes affected

ZNF117 (HGNC:12897): (zinc finger protein 117) This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Readthrough transcription occurs between this gene and the upstream endogenous retrovirus group 3 member 1 (ERV3-1) locus, and may result in additional transcript variants encoding the zinc finger protein. [provided by RefSeq, Jan 2017]

ZNF117 links:

ZNF117 (HGNC:):

ZNF117 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERV3-1-ZNF117	NM_001348050.2 linkuse as main transcript	c.1282C>T	p.Arg428*	stop_gained	4/4		NP_001334979.1
ZNF117	NM_015852.5 linkuse as main transcript	c.1282C>T	p.Arg428*	stop_gained	4/4		NP_056936.2	Q03924

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF117	ENST00000282869.11 linkuse as main transcript	c.1282C>T	p.Arg428*	stop_gained	4/4	1		ENSP00000282869.5		Q03924
ZNF117	ENST00000620222.4 linkuse as main transcript	c.1282C>T	p.Arg428*	stop_gained	3/3	1				Q03924

Frequencies

GnomAD3 genomes

AF:

0.898

AC:

135961

AN:

151468

Hom.:

61530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.767

Gnomad AMI

AF:

0.990

Gnomad AMR

AF:

0.932

Gnomad ASJ

AF:

0.975

Gnomad EAS

AF:

0.848

Gnomad SAS

AF:

0.968

Gnomad FIN

AF:

0.958

Gnomad MID

AF:

0.948

Gnomad NFE

AF:

0.953

Gnomad OTH

AF:

0.917

GnomAD3 exomes

AF:

0.934

AC:

232276

AN:

248572

Hom.:

108949

AF XY:

0.939

AC XY:

126655

AN XY:

134882

show subpopulations

Gnomad AFR exome

AF:

0.765

Gnomad AMR exome

AF:

0.934

Gnomad ASJ exome

AF:

0.977

Gnomad EAS exome

AF:

0.850

Gnomad SAS exome

AF:

0.970

Gnomad FIN exome

AF:

0.954

Gnomad NFE exome

AF:

0.954

Gnomad OTH exome

AF:

0.946

GnomAD4 exome

AF:

0.944

AC:

1378850

AN:

1461026

Hom.:

651678

Cov.:

AF XY:

0.945

AC XY:

687191

AN XY:

726840

show subpopulations

Gnomad4 AFR exome

AF:

0.763

Gnomad4 AMR exome

AF:

0.933

Gnomad4 ASJ exome

AF:

0.976

Gnomad4 EAS exome

AF:

0.852

Gnomad4 SAS exome

AF:

0.969

Gnomad4 FIN exome

AF:

0.952

Gnomad4 NFE exome

AF:

0.950

Gnomad4 OTH exome

AF:

0.937

GnomAD4 genome

AF:

0.897

AC:

136042

AN:

151588

Hom.:

61559

Cov.:

AF XY:

0.898

AC XY:

66578

AN XY:

74126

show subpopulations

Gnomad4 AFR

AF:

0.766

Gnomad4 AMR

AF:

0.932

Gnomad4 ASJ

AF:

0.975

Gnomad4 EAS

AF:

0.849

Gnomad4 SAS

AF:

0.968

Gnomad4 FIN

AF:

0.958

Gnomad4 NFE

AF:

0.953

Gnomad4 OTH

AF:

0.916

Alfa

AF:

0.944

Hom.:

20871

Bravo

AF:

0.889

TwinsUK

AF:

0.950

AC:

3522

ALSPAC

AF:

0.940

AC:

3624

ESP6500AA

AF:

0.783

AC:

3292

ESP6500EA

AF:

0.955

AC:

8119

ExAC

AF:

0.931

AC:

112710

Asia WGS

AF:

0.905

AC:

3146

AN:

3478

EpiCase

AF:

0.957

EpiControl

AF:

0.957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Uncertain

-0.020

CADD

Benign

DANN

Benign

0.88

Eigen

Benign

-0.82

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.00026

Vest4

0.041

GERP RS

-2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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