Genetic Variant ZNF839:p.Gly11Cys (chr14-102319796-G-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_018335.6(ZNF839):c.31G>T(p.Gly11Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G11R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF839
NM_018335.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

0 publications found

Variant links:

Genes affected

ZNF839 (HGNC:20345): (zinc finger protein 839) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ZNF839 links:

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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=0.18162754).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018335.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF839	NM_018335.6	MANE Select	c.31G>T	p.Gly11Cys	missense	Exon 1 of 8	NP_060805.3	A8K0R7-5
ZNF839	NM_001385065.1		c.31G>T	p.Gly11Cys	missense	Exon 1 of 7	NP_001371994.1
ZNF839	NM_001385072.1		c.31G>T	p.Gly11Cys	missense	Exon 1 of 8	NP_001372001.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF839	ENST00000442396.7	TSL:5 MANE Select	c.31G>T	p.Gly11Cys	missense	Exon 1 of 8	ENSP00000399863.2	A8K0R7-5
ZNF839	ENST00000892181.1		c.31G>T	p.Gly11Cys	missense	Exon 1 of 7	ENSP00000562240.1
ZNF839	ENST00000892182.1		c.31G>T	p.Gly11Cys	missense	Exon 1 of 8	ENSP00000562241.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1080344

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

511176

African (AFR)

AF:

0.00

AC:

AN:

22782

American (AMR)

AF:

0.00

AC:

AN:

8308

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14246

East Asian (EAS)

AF:

0.00

AC:

AN:

26372

South Asian (SAS)

AF:

0.00

AC:

AN:

20400

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21136

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3064

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

920482

Other (OTH)

AF:

0.00

AC:

AN:

43554

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.17

BayesDel_noAF

Benign

-0.49

CADD

Benign

(source)

DANN

Benign

0.81

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.40

M_CAP

Benign

0.011

MetaRNN

Benign

0.18

MetaSVM

Benign

-1.1

PhyloP100

-1.1

PrimateAI

Pathogenic

0.83

PROVEAN

Benign

-0.47

REVEL

Benign

0.025

Sift

Benign

0.11

Sift4G

Benign

0.095

Polyphen

1.0

Vest4

0.28

MutPred

0.23

Gain of catalytic residue at G16 (P = 0)

MVP

0.24

MPC

0.090

ClinPred

0.57

GERP RS

1.0

PromoterAI

-0.16

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.4

gMVP

0.14

Mutation Taster

=99/1

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

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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