Variant rs13292096 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007135.3(ZNF79):c.92C>T(p.Thr31Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 1,592,550 control chromosomes in the GnomAD database, including 276,280 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.61 ( 28264 hom., cov: 32)

Exomes 𝑓: 0.58 ( 248016 hom. )

Consequence

ZNF79
NM_007135.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0320

Variant links:

Genes affected

ZNF79 (HGNC:13153): (zinc finger protein 79) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF79 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=1.0499531E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF79	NM_007135.3 linkuse as main transcript	c.92C>T	p.Thr31Ile	missense_variant	2/5	ENST00000342483.5	NP_009066.2	Q15937

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZNF79	ENST00000342483.5 linkuse as main transcript	c.92C>T	p.Thr31Ile	missense_variant	2/5	1	NM_007135.3	ENSP00000362446.4	Q15937
ZNF79	ENST00000543471.5 linkuse as main transcript	c.20C>T	p.Thr7Ile	missense_variant	3/6	2		ENSP00000438418.1	F5H032
ZNF79	ENST00000612342.4 linkuse as main transcript	c.20C>T	p.Thr7Ile	missense_variant	2/5	2		ENSP00000478201.1	F5H032
ZNF79	ENST00000617266 linkuse as main transcript	c.-88C>T		5_prime_UTR_variant	2/3	3		ENSP00000484833.1	A0A087X2B0

Frequencies

GnomAD3 genomes

AF:

0.606

AC:

92062

AN:

151976

Hom.:

28222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.633

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.628

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.600

Gnomad OTH

AF:

0.609

GnomAD3 exomes

AF:

0.589

AC:

138547

AN:

235334

Hom.:

41678

AF XY:

0.583

AC XY:

74431

AN XY:

127698

show subpopulations

Gnomad AFR exome

AF:

0.632

Gnomad AMR exome

AF:

0.677

Gnomad ASJ exome

AF:

0.549

Gnomad EAS exome

AF:

0.383

Gnomad SAS exome

AF:

0.520

Gnomad FIN exome

AF:

0.678

Gnomad NFE exome

AF:

0.593

Gnomad OTH exome

AF:

0.600

GnomAD4 exome

AF:

0.584

AC:

840967

AN:

1440456

Hom.:

248016

Cov.:

AF XY:

0.582

AC XY:

416974

AN XY:

716466

show subpopulations

Gnomad4 AFR exome

AF:

0.641

Gnomad4 AMR exome

AF:

0.670

Gnomad4 ASJ exome

AF:

0.546

Gnomad4 EAS exome

AF:

0.386

Gnomad4 SAS exome

AF:

0.524

Gnomad4 FIN exome

AF:

0.675

Gnomad4 NFE exome

AF:

0.587

Gnomad4 OTH exome

AF:

0.575

GnomAD4 genome

AF:

0.606

AC:

92157

AN:

152094

Hom.:

28264

Cov.:

AF XY:

0.606

AC XY:

45064

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.633

Gnomad4 AMR

AF:

0.628

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.397

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.686

Gnomad4 NFE

AF:

0.600

Gnomad4 OTH

AF:

0.607

Alfa

AF:

0.593

Hom.:

56744

Bravo

AF:

0.604

TwinsUK

AF:

0.584

AC:

2166

ALSPAC

AF:

0.567

AC:

2185

ESP6500AA

AF:

0.640

AC:

2822

ESP6500EA

AF:

0.588

AC:

5061

ExAC

AF:

0.585

AC:

71041

Asia WGS

AF:

0.482

AC:

1673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.085

T;T;T

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.69

FATHMM_MKL

Benign

0.042

LIST_S2

Benign

0.13

.;T;T

MetaRNN

Benign

0.000010

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.4

.;.;M

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.97

.;N;N

REVEL

Benign

0.11

Sift

Benign

0.20

.;T;T

Sift4G

Benign

0.26

T;T;T

Polyphen

0.0010

.;.;B

Vest4

0.036

MPC

0.14

ClinPred

0.011

GERP RS

1.9

Varity_R

0.051

gMVP

0.15

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over