Variant chr9-96417699-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_153695.4(ZNF367):c.334C>A(p.Pro112Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,165,926 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00087 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0013 ( 1 hom. )

Consequence

ZNF367
NM_153695.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.440

Variant links:

Genes affected

ZNF367 (HGNC:18320): (zinc finger protein 367) Enables DNA-binding transcription factor activity. Acts upstream of or within regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF367 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.013578504).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF367	NM_153695.4 linkuse as main transcript	c.334C>A	p.Pro112Thr	missense_variant	1/5	ENST00000375256.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF367	ENST00000375256.5 linkuse as main transcript	c.334C>A	p.Pro112Thr	missense_variant	1/5	1	NM_153695.4	P1	Q7RTV3-1

Frequencies

GnomAD3 genomes

AF:

0.000873

AC:

131

AN:

150084

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000389

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000597

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000401

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00150

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00281

AC:

AN:

356

Hom.:

AF XY:

0.00431

AC XY:

AN XY:

232

show subpopulations

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00388

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00131

AC:

1334

AN:

1015740

Hom.:

Cov.:

AF XY:

0.00128

AC XY:

617

AN XY:

481194

show subpopulations

Gnomad4 AFR exome

AF:

0.0000475

Gnomad4 AMR exome

AF:

0.000670

Gnomad4 ASJ exome

AF:

0.000157

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000162

Gnomad4 FIN exome

AF:

0.000484

Gnomad4 NFE exome

AF:

0.00146

Gnomad4 OTH exome

AF:

0.00117

GnomAD4 genome

AF:

0.000872

AC:

131

AN:

150186

Hom.:

Cov.:

AF XY:

0.000914

AC XY:

AN XY:

73292

show subpopulations

Gnomad4 AFR

AF:

0.000388

Gnomad4 AMR

AF:

0.000596

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000401

Gnomad4 NFE

AF:

0.00150

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00140

Hom.:

Bravo

AF:

0.000960

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 01, 2021

The c.334C>A (p.P112T) alteration is located in exon 1 (coding exon 1) of the ZNF367 gene. This alteration results from a C to A substitution at nucleotide position 334, causing the proline (P) at amino acid position 112 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.022

Eigen

Benign

-0.099

Eigen_PC

Benign

-0.058

FATHMM_MKL

Uncertain

0.78

LIST_S2

Benign

0.37

M_CAP

Pathogenic

0.37

MetaRNN

Benign

0.014

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.90

MutationTaster

Benign

0.82

PrimateAI

Pathogenic

0.87

PROVEAN

Benign

0.24

REVEL

Benign

0.051

Sift

Uncertain

0.015

Sift4G

Benign

0.33

Polyphen

0.60

Vest4

0.17

MVP

0.093

MPC

1.2

ClinPred

0.045

GERP RS

2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Varity_R

0.070

gMVP

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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