Variant chr2-179769508-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_152520.6(ZNF385B):c.293G>T(p.Ser98Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00477 in 1,613,766 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0034 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 40 hom. )

Consequence

ZNF385B
NM_152520.6 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.66

Variant links:

Genes affected

ZNF385B (HGNC:26332): (zinc finger protein 385B) Enables p53 binding activity. Involved in intrinsic apoptotic signaling pathway by p53 class mediator. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF385B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0074246526).

BP6

Variant 2-179769508-C-A is Benign according to our data. Variant chr2-179769508-C-A is described in ClinVar as [Benign]. Clinvar id is 720664.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 40 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6 linkuse as main transcript	c.293G>T	p.Ser98Ile	missense_variant	3/10	ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7 linkuse as main transcript	c.293G>T	p.Ser98Ile	missense_variant	3/10	1	NM_152520.6	P1
ZNF385B	ENST00000451732.6 linkuse as main transcript			downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00338

AC:

514

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000941

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00340

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00704

Gnomad FIN

AF:

0.000942

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00531

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00389

AC:

972

AN:

250078

Hom.:

AF XY:

0.00447

AC XY:

605

AN XY:

135290

show subpopulations

Gnomad AFR exome

AF:

0.000617

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.0000994

Gnomad EAS exome

AF:

0.0000545

Gnomad SAS exome

AF:

0.0103

Gnomad FIN exome

AF:

0.00144

Gnomad NFE exome

AF:

0.00474

Gnomad OTH exome

AF:

0.00376

GnomAD4 exome

AF:

0.00491

AC:

7182

AN:

1461450

Hom.:

Cov.:

AF XY:

0.00507

AC XY:

3689

AN XY:

727028

show subpopulations

Gnomad4 AFR exome

AF:

0.000657

Gnomad4 AMR exome

AF:

0.00219

Gnomad4 ASJ exome

AF:

0.000344

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0106

Gnomad4 FIN exome

AF:

0.00131

Gnomad4 NFE exome

AF:

0.00522

Gnomad4 OTH exome

AF:

0.00398

GnomAD4 genome

AF:

0.00337

AC:

514

AN:

152316

Hom.:

Cov.:

AF XY:

0.00318

AC XY:

237

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.000938

Gnomad4 AMR

AF:

0.00340

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00705

Gnomad4 FIN

AF:

0.000942

Gnomad4 NFE

AF:

0.00531

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00511

Hom.:

Bravo

AF:

0.00376

TwinsUK

AF:

0.00728

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00535

AC:

ExAC

AF:

0.00415

AC:

504

Asia WGS

AF:

0.00202

AC:

AN:

3478

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	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0059

.;T

Eigen

Benign

0.080

Eigen_PC

Benign

0.20

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.39

T;T

M_CAP

Benign

0.024

MetaRNN

Benign

0.0074

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.55

.;N

MutationTaster

Benign

0.86

PrimateAI

Uncertain

0.49

REVEL

Benign

0.14

Polyphen

0.38

.;B

MVP

0.38

MPC

0.28

ClinPred

0.022

GERP RS

6.1

Varity_R

0.13

gMVP

0.33

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