Genetic Variant ZNF831:c.3738+150C>T (chr20-59194907-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_178457.3(ZNF831):c.3738+150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,145,306 control chromosomes in the GnomAD database, including 27,774 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 0.26 ( 5460 hom., cov: 33)

Exomes 𝑓: 0.21 ( 22314 hom. )

Consequence

ZNF831
NM_178457.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33

Publications

1 publications found

Variant links:

Genes affected

ZNF831 (HGNC:16167): (zinc finger protein 831) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ZNF831 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_178457.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178457.3. 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
	ZNF831	NM_178457.3	MANE Select	c.3738+150C>T		intron	N/A	NP_848552.1	Q5JPB2
	ZNF831	NM_001384354.1		c.3738+150C>T		intron	N/A	NP_001371283.1	Q5JPB2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF831	ENST00000371030.4	TSL:1 MANE Select	c.3738+150C>T		intron	N/A	ENSP00000360069.2	Q5JPB2
	ZNF831	ENST00000637017.1	TSL:5	c.3738+150C>T		intron	N/A	ENSP00000490240.1	Q5JPB2

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39406

AN:

151992

Hom.:

5458

Cov.:

show subpopulations

Gnomad AFR

AF:

0.338

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.261

GnomAD4 exome

AF:

0.206

AC:

204174

AN:

993196

Hom.:

22314

AF XY:

0.208

AC XY:

100275

AN XY:

483146

show subpopulations

African (AFR)

AF:

0.325

AC:

7222

AN:

22204

American (AMR)

AF:

0.262

AC:

3563

AN:

13588

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

3983

AN:

16024

East Asian (EAS)

AF:

0.309

AC:

9552

AN:

30944

South Asian (SAS)

AF:

0.245

AC:

9864

AN:

40244

European-Finnish (FIN)

AF:

0.225

AC:

9210

AN:

40888

Middle Eastern (MID)

AF:

0.247

AC:

718

AN:

2912

European-Non Finnish (NFE)

AF:

0.192

AC:

150665

AN:

783918

Other (OTH)

AF:

0.221

AC:

9397

AN:

42474

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

7679

15357

23036

30714

38393

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5246

10492

15738

20984

26230

<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:

0.259

AC:

39448

AN:

152110

Hom.:

5460

Cov.:

AF XY:

0.260

AC XY:

19306

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.338

AC:

14048

AN:

41512

American (AMR)

AF:

0.254

AC:

3890

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

880

AN:

3466

East Asian (EAS)

AF:

0.359

AC:

1849

AN:

5148

South Asian (SAS)

AF:

0.259

AC:

1251

AN:

4822

European-Finnish (FIN)

AF:

0.226

AC:

2389

AN:

10572

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.210

AC:

14306

AN:

67990

Other (OTH)

AF:

0.262

AC:

553

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1490

2980

4469

5959

7449

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.219

Hom.:

5446

Bravo

AF:

0.265

Asia WGS

AF:

0.320

AC:

1111

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.11

(source)

DANN

Benign

0.46

PhyloP100

-2.3

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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