Variant 14-102319771-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_018335.6(ZNF839):c.6G>T(p.Ala2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00246 in 1,230,754 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 5 hom. )

Consequence

ZNF839
NM_018335.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.04

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 14-102319771-G-T is Benign according to our data. Variant chr14-102319771-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644578.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.04 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF839	NM_018335.6 linkuse as main transcript	c.6G>T	p.Ala2=	synonymous_variant	1/8	ENST00000442396.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF839	ENST00000442396.7 linkuse as main transcript	c.6G>T	p.Ala2=	synonymous_variant	1/8	5	NM_018335.6	A2	A8K0R7-5
ZNF839	ENST00000558850.5 linkuse as main transcript	c.-61+2105G>T		intron_variant		2		P2	A8K0R7-1
ZNF839	ENST00000559185.5 linkuse as main transcript	c.-61+253G>T		intron_variant		2		P2	A8K0R7-1

Frequencies

GnomAD3 genomes

AF:

0.00171

AC:

260

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00293

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00275

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00218

AC:

AN:

1832

Hom.:

AF XY:

0.00189

AC XY:

AN XY:

1058

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad NFE exome

AF:

0.00236

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00257

AC:

2770

AN:

1078522

Hom.:

Cov.:

AF XY:

0.00260

AC XY:

1323

AN XY:

509794

show subpopulations

Gnomad4 AFR exome

AF:

0.000439

Gnomad4 AMR exome

AF:

0.000966

Gnomad4 ASJ exome

AF:

0.0000704

Gnomad4 EAS exome

AF:

0.0000380

Gnomad4 SAS exome

AF:

0.000299

Gnomad4 FIN exome

AF:

0.00294

Gnomad4 NFE exome

AF:

0.00280

Gnomad4 OTH exome

AF:

0.00228

GnomAD4 genome

AF:

0.00171

AC:

260

AN:

152232

Hom.:

Cov.:

AF XY:

0.00157

AC XY:

117

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.000654

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00293

Gnomad4 NFE

AF:

0.00275

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00249

Hom.:

Bravo

AF:

0.00147

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

ZNF839: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over