Genetic Variant ZNF782:c.15+125C>T (chr9-96851822-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001001662.3(ZNF782):c.15+125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 1,003,056 control chromosomes in the GnomAD database, including 10,953 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 5064 hom., cov: 32)

Exomes 𝑓: 0.057 ( 5889 hom. )

Consequence

ZNF782
NM_001001662.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.385

Publications

6 publications found

Variant links:

Genes affected

ZNF782 (HGNC:33110): (zinc finger protein 782) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific 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]

ZNF782 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001662.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF782	NM_001001662.3	MANE Select	c.15+125C>T	intron	N/A	NP_001001662.1	Q6ZMW2
ZNF782	NM_001346991.2		c.15+125C>T	intron	N/A	NP_001333920.1	Q6ZMW2
ZNF782	NM_001346993.2		c.-58+2266C>T	intron	N/A	NP_001333922.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF782	ENST00000481138.6	TSL:1 MANE Select	c.15+125C>T	intron	N/A	ENSP00000419397.1	Q6ZMW2
ZNF782	ENST00000535338.5	TSL:3	c.15+125C>T	intron	N/A	ENSP00000440624.2	Q6ZMW2
ZNF782	ENST00000917517.1		c.15+125C>T	intron	N/A	ENSP00000587576.1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25207

AN:

152000

Hom.:

5027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0770

Gnomad ASJ

AF:

0.0245

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.0923

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.114

GnomAD4 exome

AF:

0.0569

AC:

48421

AN:

850938

Hom.:

5889

AF XY:

0.0569

AC XY:

25075

AN XY:

441026

show subpopulations

African (AFR)

AF:

0.476

AC:

9816

AN:

20626

American (AMR)

AF:

0.0543

AC:

1848

AN:

34050

Ashkenazi Jewish (ASJ)

AF:

0.0260

AC:

501

AN:

19294

East Asian (EAS)

AF:

0.374

AC:

13144

AN:

35138

South Asian (SAS)

AF:

0.110

AC:

6867

AN:

62294

European-Finnish (FIN)

AF:

0.0834

AC:

3723

AN:

44650

Middle Eastern (MID)

AF:

0.0687

AC:

299

AN:

4354

European-Non Finnish (NFE)

AF:

0.0154

AC:

9113

AN:

590814

Other (OTH)

AF:

0.0783

AC:

3110

AN:

39718

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1724

3448

5173

6897

8621

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

524

1048

1572

2096

2620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.166

AC:

25284

AN:

152118

Hom.:

5064

Cov.:

AF XY:

0.169

AC XY:

12573

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.466

AC:

19325

AN:

41460

American (AMR)

AF:

0.0768

AC:

1173

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0245

AC:

AN:

3468

East Asian (EAS)

AF:

0.341

AC:

1766

AN:

5174

South Asian (SAS)

AF:

0.115

AC:

555

AN:

4812

European-Finnish (FIN)

AF:

0.0923

AC:

977

AN:

10590

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0166

AC:

1128

AN:

68014

Other (OTH)

AF:

0.113

AC:

239

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

773

1547

2320

3094

3867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.122

Hom.:

649

Bravo

AF:

0.179

Asia WGS

AF:

0.198

AC:

689

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.15

(source)

DANN

Benign

0.54

PhyloP100

-0.39

Mutation Taster

=100/0

polymorphism (auto)

(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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over