Variant chr19-34684687-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000505242.6(ZNF302):c.650G>A(p.Ser217Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,613,732 control chromosomes in the GnomAD database, including 14,840 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S217G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.11 ( 1172 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13668 hom. )

Consequence

ZNF302
ENST00000505242.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.839

Variant links:

Genes affected

ZNF302 (HGNC:13848): (zinc finger protein 302) This gene encodes a member of the zinc-finger protein family. The encoded protein contains seven C2H2-type zinc fingers and a KRAB domain, but its function has yet to be determined. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2014]

ZNF302 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038046837).

BP6

Variant 19-34684687-G-A is Benign according to our data. Variant chr19-34684687-G-A is described in ClinVar as [Benign]. Clinvar id is 770809.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF302	NM_001289187.2 linkuse as main transcript	c.650G>A	p.Ser217Asn	missense_variant	5/5	ENST00000505242.6	NP_001276116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF302	ENST00000505242.6 linkuse as main transcript	c.650G>A	p.Ser217Asn	missense_variant	5/5	1	NM_001289187.2	ENSP00000421028	P4	Q9NR11-2

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17350

AN:

151992

Hom.:

1171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0854

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.0704

Gnomad SAS

AF:

0.260

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.134

GnomAD3 exomes

AF:

0.133

AC:

33267

AN:

250318

Hom.:

2689

AF XY:

0.142

AC XY:

19327

AN XY:

135694

show subpopulations

Gnomad AFR exome

AF:

0.0754

Gnomad AMR exome

AF:

0.0718

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.0712

Gnomad SAS exome

AF:

0.255

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.132

Gnomad OTH exome

AF:

0.148

GnomAD4 exome

AF:

0.129

AC:

188429

AN:

1461622

Hom.:

13668

Cov.:

AF XY:

0.134

AC XY:

97195

AN XY:

727086

show subpopulations

Gnomad4 AFR exome

AF:

0.0764

Gnomad4 AMR exome

AF:

0.0729

Gnomad4 ASJ exome

AF:

0.163

Gnomad4 EAS exome

AF:

0.0497

Gnomad4 SAS exome

AF:

0.258

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.114

AC:

17362

AN:

152110

Hom.:

1172

Cov.:

AF XY:

0.116

AC XY:

8615

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.0771

Gnomad4 AMR

AF:

0.0854

Gnomad4 ASJ

AF:

0.162

Gnomad4 EAS

AF:

0.0707

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.134

Alfa

AF:

0.125

Hom.:

538

Bravo

AF:

0.108

ESP6500AA

AF:

0.0710

AC:

312

ESP6500EA

AF:

0.130

AC:

1116

ExAC

AF:

0.136

AC:

16482

EpiCase

AF:

0.139

EpiControl

AF:

0.135

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.86

BayesDel_noAF

Benign

-0.86

CADD

Benign

9.0

DANN

Benign

0.60

DEOGEN2

Benign

0.0032

T;T;.;.;.;.

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.023

T;T;.;.;T;T

MetaRNN

Benign

0.0038

T;T;T;T;T;T

MetaSVM

Benign

-0.95

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.60

.;.;N;N;N;N

REVEL

Benign

0.016

Sift

Benign

0.44

.;.;T;T;T;T

Sift4G

Benign

0.56

T;T;T;T;T;T

Polyphen

0.0

.;.;B;B;B;B

Vest4

0.011

MPC

0.047

ClinPred

0.000030

GERP RS

-0.10

gMVP

0.018

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