Variant 19-36341048-C-G 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 NM_020917.3(ZFP14):c.778G>C(p.Glu260Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,614,032 control chromosomes in the GnomAD database, including 269 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 146 hom., cov: 32)

Exomes 𝑓: 0.0023 ( 123 hom. )

Consequence

ZFP14
NM_020917.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.334

Variant links:

Genes affected

ZFP14 (HGNC:29312): (ZFP14 zinc finger protein) 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. Predicted to act upstream of or within blastocyst hatching. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZFP14 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=0.0017897487).

BP6

Variant 19-36341048-C-G is Benign according to our data. Variant chr19-36341048-C-G is described in ClinVar as [Benign]. Clinvar id is 783829.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.08 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFP14	NM_020917.3 linkuse as main transcript	c.778G>C	p.Glu260Gln	missense_variant	5/5	ENST00000270001.12	NP_065968.1
ZFP14	NM_001297619.2 linkuse as main transcript	c.781G>C	p.Glu261Gln	missense_variant	5/5		NP_001284548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFP14	ENST00000270001.12 linkuse as main transcript	c.778G>C	p.Glu260Gln	missense_variant	5/5	1	NM_020917.3	ENSP00000270001	P1

Frequencies

GnomAD3 genomes

AF:

0.0238

AC:

3614

AN:

152076

Hom.:

146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0824

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00989

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.0167

GnomAD3 exomes

AF:

0.00626

AC:

1574

AN:

251290

Hom.:

AF XY:

0.00447

AC XY:

607

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.0835

Gnomad AMR exome

AF:

0.00544

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000980

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000123

Gnomad OTH exome

AF:

0.00261

GnomAD4 exome

AF:

0.00231

AC:

3375

AN:

1461840

Hom.:

123

Cov.:

AF XY:

0.00189

AC XY:

1378

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.0822

Gnomad4 AMR exome

AF:

0.00577

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000927

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000486

Gnomad4 OTH exome

AF:

0.00470

GnomAD4 genome

AF:

0.0238

AC:

3620

AN:

152192

Hom.:

146

Cov.:

AF XY:

0.0226

AC XY:

1679

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0823

Gnomad4 AMR

AF:

0.00988

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000250

Gnomad4 OTH

AF:

0.0166

Alfa

AF:

0.00369

Hom.:

Bravo

AF:

0.0266

ESP6500AA

AF:

0.0785

AC:

346

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00777

AC:

943

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.0000593

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 24, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.67

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.061

Eigen

Benign

0.12

Eigen_PC

Benign

0.069

FATHMM_MKL

Benign

0.030

LIST_S2

Benign

0.18

MetaRNN

Benign

0.0018

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.025

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.59

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.16

Sift

Benign

0.11

Sift4G

Benign

0.42

Polyphen

0.96

Vest4

0.091

MVP

0.17

MPC

1.2

ClinPred

0.038

GERP RS

4.1

Varity_R

0.22

gMVP

0.094

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