Variant rs324125 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001145434.2(ZNF880):c.449A>G(p.Tyr150Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,555,352 control chromosomes in the GnomAD database, including 14,987 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2191 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12796 hom. )

Consequence

ZNF880
NM_001145434.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.219

Variant links:

Genes affected

ZNF880 (HGNC:37249): (zinc finger protein 880) 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF880 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005609393).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF880	NM_001145434.2 link	c.449A>G	p.Tyr150Cys	missense_variant	4/4	ENST00000422689.3	NP_001138906.1	Q6PDB4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF880	ENST00000422689.3 link	c.449A>G	p.Tyr150Cys	missense_variant	4/4	2	NM_001145434.2	ENSP00000406318.2		Q6PDB4-1

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24570

AN:

152056

Hom.:

2195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.0887

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.160

GnomAD3 exomes

AF:

0.127

AC:

20721

AN:

163008

Hom.:

1419

AF XY:

0.126

AC XY:

10926

AN XY:

86560

show subpopulations

Gnomad AFR exome

AF:

0.244

Gnomad AMR exome

AF:

0.0944

Gnomad ASJ exome

AF:

0.168

Gnomad EAS exome

AF:

0.118

Gnomad SAS exome

AF:

0.0889

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.130

GnomAD4 exome

AF:

0.132

AC:

184890

AN:

1403178

Hom.:

12796

Cov.:

AF XY:

0.131

AC XY:

90605

AN XY:

692726

show subpopulations

Gnomad4 AFR exome

AF:

0.248

Gnomad4 AMR exome

AF:

0.0968

Gnomad4 ASJ exome

AF:

0.171

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.0874

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.132

Gnomad4 OTH exome

AF:

0.138

GnomAD4 genome

AF:

0.162

AC:

24584

AN:

152174

Hom.:

2191

Cov.:

AF XY:

0.158

AC XY:

11747

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.172

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.0888

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.137

Hom.:

3796

Bravo

AF:

0.163

TwinsUK

AF:

0.128

AC:

474

ALSPAC

AF:

0.126

AC:

485

ESP6500AA

AF:

0.236

AC:

327

ESP6500EA

AF:

0.143

AC:

454

ExAC

AF:

0.0867

AC:

9221

Asia WGS

AF:

0.114

AC:

397

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.0

DANN

Benign

0.88

DEOGEN2

Benign

0.0034

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0091

LIST_S2

Benign

0.086

MetaRNN

Benign

0.0056

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.0

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.2

REVEL

Benign

0.017

Sift

Benign

0.17

Sift4G

Benign

0.17

Polyphen

0.017

Vest4

0.040

MPC

0.21

ClinPred

0.00074

GERP RS

-2.9

Varity_R

0.042

gMVP

0.034

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over