Variant 3-75741362-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001290208.3(ZNF717):c.191A>G(p.Tyr64Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 1,515,380 control chromosomes in the GnomAD database, including 531,993 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.85 ( 53023 hom., cov: 38)

Exomes 𝑓: 0.84 ( 478970 hom. )

Consequence

ZNF717
NM_001290208.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.90

Variant links:

Genes affected

ZNF717 (HGNC:29448): (zinc finger protein 717) This gene encodes a Kruppel-associated box (KRAB) zinc-finger protein, which belongs to a large group of transcriptional regulators in mammals. These proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation and apoptosis, and in regulating viral replication and transcription. A pseudogene of this gene was identified on chromosome 1. [provided by RefSeq, May 2016]

ZNF717 links:

LINC00960 (HGNC:48710): (long intergenic non-protein coding RNA 960)

LINC00960 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0067239106).

BP6

Variant 3-75741362-T-C is Benign according to our data. Variant chr3-75741362-T-C is described in ClinVar as [Benign]. Clinvar id is 769608.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF717	NM_001290208.3 linkuse as main transcript	c.191A>G	p.Tyr64Cys	missense_variant	4/5	ENST00000652011.2	NP_001277137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF717	ENST00000652011.2 linkuse as main transcript	c.191A>G	p.Tyr64Cys	missense_variant	4/5		NM_001290208.3	ENSP00000498738	P1
LINC00960	ENST00000668145.1 linkuse as main transcript	n.1240T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.846

AC:

127974

AN:

151218

Hom.:

52968

Cov.:

show subpopulations

Gnomad AFR

AF:

0.839

Gnomad AMI

AF:

0.888

Gnomad AMR

AF:

0.867

Gnomad ASJ

AF:

0.844

Gnomad EAS

AF:

0.894

Gnomad SAS

AF:

0.868

Gnomad FIN

AF:

0.810

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.845

Gnomad OTH

AF:

0.867

GnomAD3 exomes

AF:

0.0000437

AC:

AN:

45734

Hom.:

AF XY:

0.0000414

AC XY:

AN XY:

24162

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000342

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.844

AC:

1151530

AN:

1364046

Hom.:

478970

Cov.:

AF XY:

0.845

AC XY:

569602

AN XY:

673924

show subpopulations

Gnomad4 AFR exome

AF:

0.845

Gnomad4 AMR exome

AF:

0.857

Gnomad4 ASJ exome

AF:

0.841

Gnomad4 EAS exome

AF:

0.900

Gnomad4 SAS exome

AF:

0.865

Gnomad4 FIN exome

AF:

0.807

Gnomad4 NFE exome

AF:

0.841

Gnomad4 OTH exome

AF:

0.855

GnomAD4 genome

AF:

0.846

AC:

128085

AN:

151334

Hom.:

53023

Cov.:

AF XY:

0.846

AC XY:

62615

AN XY:

74002

show subpopulations

Gnomad4 AFR

AF:

0.839

Gnomad4 AMR

AF:

0.867

Gnomad4 ASJ

AF:

0.844

Gnomad4 EAS

AF:

0.894

Gnomad4 SAS

AF:

0.868

Gnomad4 FIN

AF:

0.810

Gnomad4 NFE

AF:

0.845

Gnomad4 OTH

AF:

0.867

Alfa

AF:

0.837

Hom.:

9561

ExAC

AF:

0.0109

AC:

107

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.74

DANN

Benign

0.62

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0012

LIST_S2

Benign

0.015

T;T;T;T

M_CAP

Benign

0.00064

MetaRNN

Benign

0.0067

T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.47

PROVEAN

Benign

9.2

N;N;N;N

REVEL

Benign

0.024

Sift

Benign

1.0

T;T;T;T

Sift4G

Benign

0.64

T;T;.;.

Vest4

0.082

ClinPred

0.042

GERP RS

-2.6

gMVP

0.0067

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over