Genetic Variant NM_175872.5:c.1587C>T (chr19-34958268-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_175872.5(ZNF792):c.1587C>T(p.Thr529Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00625 in 1,603,382 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0064 ( 41 hom. )

Consequence

ZNF792
NM_175872.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -8.41

Publications

3 publications found

Variant links:

Genes affected

ZNF792 (HGNC:24751): (zinc finger protein 792) Enables identical protein 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]

ZNF792 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 19-34958268-G-A is Benign according to our data. Variant chr19-34958268-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2649711.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-8.41 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF792	NM_175872.5 link	c.1587C>T	p.Thr529Thr	synonymous_variant	Exon 4 of 4	ENST00000404801.2	NP_787068.3	Q3KQV3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF792	ENST00000404801.2 link	c.1587C>T	p.Thr529Thr	synonymous_variant	Exon 4 of 4	2	NM_175872.5	ENSP00000385099.1		Q3KQV3
ZNF792	ENST00000605484.1 link	c.1386C>T	p.Thr462Thr	synonymous_variant	Exon 2 of 2	1		ENSP00000474130.1		S4R3B8

Frequencies

GnomAD3 genomes

AF:

0.00513

AC:

741

AN:

144498

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00349

Gnomad ASJ

AF:

0.0126

Gnomad EAS

AF:

0.000208

Gnomad SAS

AF:

0.00135

Gnomad FIN

AF:

0.00202

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00860

Gnomad OTH

AF:

0.00617

GnomAD2 exomes

AF:

0.00463

AC:

1161

AN:

250710

AF XY:

0.00454

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00325

Gnomad ASJ exome

AF:

0.0120

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.00711

Gnomad OTH exome

AF:

0.00589

GnomAD4 exome

AF:

0.00637

AC:

9287

AN:

1458762

Hom.:

Cov.:

AF XY:

0.00631

AC XY:

4577

AN XY:

725602

show subpopulations

African (AFR)

AF:

0.00132

AC:

AN:

33360

American (AMR)

AF:

0.00331

AC:

146

AN:

44096

Ashkenazi Jewish (ASJ)

AF:

0.0118

AC:

307

AN:

26032

East Asian (EAS)

AF:

0.000102

AC:

AN:

39356

South Asian (SAS)

AF:

0.000912

AC:

AN:

85570

European-Finnish (FIN)

AF:

0.00228

AC:

122

AN:

53392

Middle Eastern (MID)

AF:

0.00226

AC:

AN:

5754

European-Non Finnish (NFE)

AF:

0.00740

AC:

8218

AN:

1110930

Other (OTH)

AF:

0.00589

AC:

355

AN:

60272

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

587

1174

1761

2348

2935

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00512

AC:

741

AN:

144620

Hom.:

Cov.:

AF XY:

0.00476

AC XY:

337

AN XY:

70766

show subpopulations

African (AFR)

AF:

0.00118

AC:

AN:

38960

American (AMR)

AF:

0.00348

AC:

AN:

14644

Ashkenazi Jewish (ASJ)

AF:

0.0126

AC:

AN:

3346

East Asian (EAS)

AF:

0.000208

AC:

AN:

4802

South Asian (SAS)

AF:

0.00135

AC:

AN:

4430

European-Finnish (FIN)

AF:

0.00202

AC:

AN:

9908

Middle Eastern (MID)

AF:

0.00

AC:

AN:

244

European-Non Finnish (NFE)

AF:

0.00860

AC:

563

AN:

65454

Other (OTH)

AF:

0.00610

AC:

AN:

1968

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

121

162

202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00717

Hom.:

EpiCase

AF:

0.00606

EpiControl

AF:

0.00694

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

ZNF792: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.4

(source)

DANN

Benign

0.88

PhyloP100

-8.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

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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NM_175872.5:c.1587C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over