Variant rs3217319 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_144684.4(ZNF480):c.9_10del(p.Cys3Ter) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 1,612,698 control chromosomes in the GnomAD database, including 415,545 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.63 ( 31645 hom., cov: 0)

Exomes 𝑓: 0.72 ( 383900 hom. )

Consequence

ZNF480
NM_144684.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0310

Variant links:

Genes affected

ZNF480 (HGNC:23305): (zinc finger protein 480) 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. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF480 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 19-52300416-CTG-C is Benign according to our data. Variant chr19-52300416-CTG-C is described in ClinVar as [Benign]. Clinvar id is 403625.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ZNF480	NM_144684.4 linkuse as main transcript	c.9_10del	p.Cys3Ter	frameshift_variant	2/5	ENST00000595962.6	NP_653285.2
ZNF480	NM_001297624.2 linkuse as main transcript	c.9_10del	p.Cys3Ter	frameshift_variant	2/4		NP_001284553.1
ZNF480	NM_001297625.2 linkuse as main transcript	c.-96_-95del		5_prime_UTR_variant	2/4		NP_001284554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF480	ENST00000595962.6 linkuse as main transcript	c.9_10del	p.Cys3Ter	frameshift_variant	2/5	1	NM_144684.4	ENSP00000471754	P1	Q8WV37-1

Frequencies

GnomAD3 genomes

AF:

0.629

AC:

95257

AN:

151508

Hom.:

31650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.742

Gnomad FIN

AF:

0.784

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.733

Gnomad OTH

AF:

0.642

GnomAD3 exomes

AF:

0.691

AC:

173530

AN:

251220

Hom.:

61168

AF XY:

0.701

AC XY:

95241

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.379

Gnomad AMR exome

AF:

0.663

Gnomad ASJ exome

AF:

0.632

Gnomad EAS exome

AF:

0.631

Gnomad SAS exome

AF:

0.728

Gnomad FIN exome

AF:

0.774

Gnomad NFE exome

AF:

0.732

Gnomad OTH exome

AF:

0.702

GnomAD4 exome

AF:

0.722

AC:

1054817

AN:

1461072

Hom.:

383900

AF XY:

0.722

AC XY:

525143

AN XY:

726888

show subpopulations

Gnomad4 AFR exome

AF:

0.374

Gnomad4 AMR exome

AF:

0.664

Gnomad4 ASJ exome

AF:

0.635

Gnomad4 EAS exome

AF:

0.664

Gnomad4 SAS exome

AF:

0.729

Gnomad4 FIN exome

AF:

0.768

Gnomad4 NFE exome

AF:

0.738

Gnomad4 OTH exome

AF:

0.695

GnomAD4 genome

AF:

0.628

AC:

95265

AN:

151626

Hom.:

31645

Cov.:

AF XY:

0.634

AC XY:

46961

AN XY:

74060

show subpopulations

Gnomad4 AFR

AF:

0.386

Gnomad4 AMR

AF:

0.671

Gnomad4 ASJ

AF:

0.635

Gnomad4 EAS

AF:

0.629

Gnomad4 SAS

AF:

0.743

Gnomad4 FIN

AF:

0.784

Gnomad4 NFE

AF:

0.733

Gnomad4 OTH

AF:

0.640

Alfa

AF:

0.675

Hom.:

6504

Bravo

AF:

0.609

Asia WGS

AF:

0.631

AC:

2193

AN:

3478

EpiCase

AF:

0.722

EpiControl

AF:

0.729

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 7679/12518=61.35% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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