Genetic Variant ZNF787:p.Gly250Ser (chr19-56088424-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001002836.4(ZNF787):c.748G>A(p.Gly250Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 146,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000068 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF787
NM_001002836.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.220

Publications

0 publications found

Variant links:

Genes affected

ZNF787 (HGNC:26998): (zinc finger protein 787) Enables sequence-specific double-stranded 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]

ZNF787 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.11606032).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002836.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF787	NM_001002836.4	MANE Select	c.748G>A	p.Gly250Ser	missense	Exon 3 of 3	NP_001002836.2	Q6DD87

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF787	ENST00000610935.2	TSL:1 MANE Select	c.748G>A	p.Gly250Ser	missense	Exon 3 of 3	ENSP00000478557.1	Q6DD87
ZNF787	ENST00000969467.1		c.748G>A	p.Gly250Ser	missense	Exon 3 of 3	ENSP00000639526.1
ZNF787	ENST00000969468.1		c.748G>A	p.Gly250Ser	missense	Exon 4 of 4	ENSP00000639527.1

Frequencies

GnomAD3 genomes

AF:

0.00000684

AC:

AN:

146214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000678

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1020592

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

482434

African (AFR)

AF:

0.00

AC:

AN:

19952

American (AMR)

AF:

0.00

AC:

AN:

5976

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10926

East Asian (EAS)

AF:

0.00

AC:

AN:

18656

South Asian (SAS)

AF:

0.00

AC:

AN:

23326

European-Finnish (FIN)

AF:

0.00

AC:

AN:

19982

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2532

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

880694

Other (OTH)

AF:

0.00

AC:

AN:

38548

GnomAD4 genome

AF:

0.00000684

AC:

AN:

146214

Hom.:

Cov.:

AF XY:

0.0000140

AC XY:

AN XY:

71244

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

40418

American (AMR)

AF:

0.0000678

AC:

AN:

14754

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3388

East Asian (EAS)

AF:

0.00

AC:

AN:

4980

South Asian (SAS)

AF:

0.00

AC:

AN:

4760

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8708

Middle Eastern (MID)

AF:

0.00

AC:

AN:

302

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

65990

Other (OTH)

AF:

0.00

AC:

AN:

2030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000189

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.025

Eigen

Benign

-0.53

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.038

LIST_S2

Benign

0.61

M_CAP

Uncertain

0.26

MetaRNN

Benign

0.12

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.69

PhyloP100

-0.22

PrimateAI

Pathogenic

0.86

Sift4G

Benign

0.079

Polyphen

0.26

Vest4

0.038

MutPred

0.38

Gain of glycosylation at G250 (P = 0.0021)

MVP

0.043

ClinPred

0.31

GERP RS

3.7

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

3.5

Varity_R

0.083

gMVP

0.15

Mutation Taster

=98/2

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over