Variant 9-65679226-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000382405.8(ZNG1E):c.215C>T(p.Ala72Val) variant causes a missense change. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0067 ( 0 hom., cov: 18)

Exomes 𝑓: 0.00056 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNG1E
ENST00000382405.8 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.89

Variant links:

Genes affected

ZNG1E (HGNC:24584): (Zn regulated GTPase metalloprotein activator 1E) Predicted to enable ATP binding activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNG1E links:

ZNG1E (HGNC:):

ZNG1E links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 9-65679226-C-T is Benign according to our data. Variant chr9-65679226-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3199139.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNG1E	NM_001330668.2 linkuse as main transcript	c.215C>T	p.Ala72Val	missense_variant	2/15	ENST00000382405.8	NP_001317597.1	Q5RIA9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNG1E	ENST00000382405.8 linkuse as main transcript	c.215C>T	p.Ala72Val	missense_variant	2/15	1	NM_001330668.2	ENSP00000371842.3		Q5RIA9-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

885

AN:

132788

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0252

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00146

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:

0.0000627

Gnomad OTH

AF:

0.00530

GnomAD3 exomes

AF:

0.00202

AC:

AN:

20320

Hom.:

AF XY:

0.00167

AC XY:

AN XY:

10752

show subpopulations

Gnomad AFR exome

AF:

0.0281

Gnomad AMR exome

AF:

0.000530

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000307

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000556

AC:

277

AN:

497912

Hom.:

Cov.:

AF XY:

0.000463

AC XY:

120

AN XY:

259284

show subpopulations

Gnomad4 AFR exome

AF:

0.0180

Gnomad4 AMR exome

AF:

0.00120

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000718

Gnomad4 SAS exome

AF:

0.0000271

Gnomad4 FIN exome

AF:

0.0000283

Gnomad4 NFE exome

AF:

0.0000121

Gnomad4 OTH exome

AF:

0.00149

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00667

AC:

886

AN:

132868

Hom.:

Cov.:

AF XY:

0.00661

AC XY:

419

AN XY:

63392

show subpopulations

Gnomad4 AFR

AF:

0.0251

Gnomad4 AMR

AF:

0.00146

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000627

Gnomad4 OTH

AF:

0.00524

Alfa

AF:

0.00540

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 12, 2021

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.51

BayesDel_noAF

Pathogenic

0.31

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

T;.;.;.;.

LIST_S2

Pathogenic

1.0

D;D;D;D;D

MetaRNN

Uncertain

0.70

D;D;D;D;D

PROVEAN

Uncertain

-3.4

D;D;D;D;D

Sift

Benign

0.042

D;D;D;D;D

Sift4G

Uncertain

0.056

T;D;T;T;T

Vest4

0.75

gMVP

0.76

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