Variant chr19-21727323-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_173531.4(ZNF100):c.989C>A(p.Ser330*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00936 in 1,609,488 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0080 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0095 ( 125 hom. )

Consequence

ZNF100
NM_173531.4 stop_gained

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.00400

Variant links:

Genes affected

ZNF100 (HGNC:12880): (zinc finger protein 100) 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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF100 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF100	NM_173531.4 linkuse as main transcript	c.989C>A	p.Ser330*	stop_gained	5/5	ENST00000358296.11	NP_775802.2	Q8IYN0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF100	ENST00000358296.11 linkuse as main transcript	c.989C>A	p.Ser330*	stop_gained	5/5	1	NM_173531.4	ENSP00000351042.5		Q8IYN0
ZNF100	ENST00000305570.10 linkuse as main transcript	c.797C>A	p.Ser266*	stop_gained	4/4	1		ENSP00000445201.3		A0A0A0MTN5

Frequencies

GnomAD3 genomes

AF:

0.00806

AC:

1225

AN:

151906

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00167

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00996

Gnomad ASJ

AF:

0.00894

Gnomad EAS

AF:

0.00577

Gnomad SAS

AF:

0.00620

Gnomad FIN

AF:

0.00879

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.0117

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.00903

AC:

2242

AN:

248376

Hom.:

AF XY:

0.00893

AC XY:

1205

AN XY:

134882

show subpopulations

Gnomad AFR exome

AF:

0.00162

Gnomad AMR exome

AF:

0.00608

Gnomad ASJ exome

AF:

0.00956

Gnomad EAS exome

AF:

0.0100

Gnomad SAS exome

AF:

0.00471

Gnomad FIN exome

AF:

0.00817

Gnomad NFE exome

AF:

0.0120

Gnomad OTH exome

AF:

0.00990

GnomAD4 exome

AF:

0.00949

AC:

13835

AN:

1457464

Hom.:

125

Cov.:

AF XY:

0.00952

AC XY:

6903

AN XY:

725180

show subpopulations

Gnomad4 AFR exome

AF:

0.00165

Gnomad4 AMR exome

AF:

0.00593

Gnomad4 ASJ exome

AF:

0.00873

Gnomad4 EAS exome

AF:

0.00766

Gnomad4 SAS exome

AF:

0.00533

Gnomad4 FIN exome

AF:

0.00940

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.00886

GnomAD4 genome

AF:

0.00804

AC:

1223

AN:

152024

Hom.:

Cov.:

AF XY:

0.00831

AC XY:

618

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00995

Gnomad4 ASJ

AF:

0.00894

Gnomad4 EAS

AF:

0.00578

Gnomad4 SAS

AF:

0.00621

Gnomad4 FIN

AF:

0.00879

Gnomad4 NFE

AF:

0.0117

Gnomad4 OTH

AF:

0.00757

Alfa

AF:

0.00706

Hom.:

Bravo

AF:

0.00816

TwinsUK

AF:

0.0108

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00273

AC:

ESP6500EA

AF:

0.0126

AC:

108

ExAC

AF:

0.00983

AC:

1193

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.0135

EpiControl

AF:

0.0131

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	Apr 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.021

BayesDel_noAF

Pathogenic

0.21

CADD

Pathogenic

DANN

Benign

0.95

Eigen

Benign

0.038

Eigen_PC

Benign

-0.30

FATHMM_MKL

Benign

0.00022

Vest4

0.047

GERP RS

-0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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