Variant chr19-2936537-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP5BA1

The NM_021217.3(ZNF77):c.298C>T(p.Gln100Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0435 in 1,601,876 control chromosomes in the GnomAD database, including 1,731 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Pathogenic (no stars).

Frequency

Genomes: 𝑓 0.034 ( 118 hom., cov: 33)

Exomes 𝑓: 0.045 ( 1613 hom. )

Consequence

ZNF77
NM_021217.3 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0480

Variant links:

Genes affected

ZNF77 (HGNC:13150): (zinc finger protein 77) 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]

ZNF77 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PP5

Variant 19-2936537-G-A is Pathogenic according to our data. Variant chr19-2936537-G-A is described in Lovd as [Pathogenic].

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ZNF77	NM_021217.3 linkuse as main transcript	c.298C>T	p.Gln100Ter	stop_gained	3/4	ENST00000314531.5	NP_067040.1
ZNF77	XM_047439170.1 linkuse as main transcript	c.202C>T	p.Gln68Ter	stop_gained	3/4		XP_047295126.1
ZNF77	XM_017027081.2 linkuse as main transcript	c.-243C>T		5_prime_UTR_variant	2/3		XP_016882570.1
ZNF77	XM_047439171.1 linkuse as main transcript	c.-243C>T		5_prime_UTR_variant	2/3		XP_047295127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF77	ENST00000314531.5 linkuse as main transcript	c.298C>T	p.Gln100Ter	stop_gained	3/4	1	NM_021217.3	ENSP00000319053	P1

Frequencies

GnomAD3 genomes

AF:

0.0339

AC:

5156

AN:

152170

Hom.:

117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0205

Gnomad AMI

AF:

0.0637

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0553

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0201

Gnomad FIN

AF:

0.0153

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0331

GnomAD3 exomes

AF:

0.0311

AC:

7408

AN:

238526

Hom.:

164

AF XY:

0.0319

AC XY:

4129

AN XY:

129358

show subpopulations

Gnomad AFR exome

AF:

0.0185

Gnomad AMR exome

AF:

0.0149

Gnomad ASJ exome

AF:

0.0556

Gnomad EAS exome

AF:

0.000169

Gnomad SAS exome

AF:

0.0225

Gnomad FIN exome

AF:

0.0140

Gnomad NFE exome

AF:

0.0457

Gnomad OTH exome

AF:

0.0293

GnomAD4 exome

AF:

0.0446

AC:

64582

AN:

1449588

Hom.:

1613

Cov.:

AF XY:

0.0437

AC XY:

31547

AN XY:

721164

show subpopulations

Gnomad4 AFR exome

AF:

0.0198

Gnomad4 AMR exome

AF:

0.0162

Gnomad4 ASJ exome

AF:

0.0588

Gnomad4 EAS exome

AF:

0.000128

Gnomad4 SAS exome

AF:

0.0217

Gnomad4 FIN exome

AF:

0.0149

Gnomad4 NFE exome

AF:

0.0512

Gnomad4 OTH exome

AF:

0.0383

GnomAD4 genome

AF:

0.0339

AC:

5160

AN:

152288

Hom.:

118

Cov.:

AF XY:

0.0319

AC XY:

2374

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0205

Gnomad4 AMR

AF:

0.0223

Gnomad4 ASJ

AF:

0.0553

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0207

Gnomad4 FIN

AF:

0.0153

Gnomad4 NFE

AF:

0.0496

Gnomad4 OTH

AF:

0.0327

Alfa

AF:

0.0442

Hom.:

297

Bravo

AF:

0.0330

TwinsUK

AF:

0.0526

AC:

195

ALSPAC

AF:

0.0464

AC:

179

ESP6500AA

AF:

0.0204

AC:

ESP6500EA

AF:

0.0437

AC:

376

ExAC

AF:

0.0309

AC:

3752

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.24

CADD

Pathogenic

DANN

Benign

0.94

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.97

FATHMM_MKL

Benign

0.026

MutationTaster

Benign

1.0

Vest4

0.022

GERP RS

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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