dbSNP rs3217: ZNF518B:c.*78G>A (chr4-10443026-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_053042.3(ZNF518B):c.*78G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,276,302 control chromosomes in the GnomAD database, including 83,831 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 0.28 ( 7122 hom., cov: 33)

Exomes 𝑓: 0.36 ( 76709 hom. )

Consequence

ZNF518B
NM_053042.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

Publications

12 publications found

Variant links:

Genes affected

ZNF518B (HGNC:29365): (zinc finger protein 518B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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]

ZNF518B Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ZNF518B 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF518B	NM_053042.3 link	c.*78G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000326756.4	NP_444270.2	Q9C0D4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF518B	ENST00000326756.4 link	c.*78G>A		3_prime_UTR_variant	Exon 3 of 3	3	NM_053042.3	ENSP00000317614.3		Q9C0D4

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42584

AN:

152028

Hom.:

7119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.362

AC:

406737

AN:

1124156

Hom.:

76709

Cov.:

AF XY:

0.359

AC XY:

201256

AN XY:

561338

show subpopulations

African (AFR)

AF:

0.0997

AC:

2556

AN:

25642

American (AMR)

AF:

0.212

AC:

5850

AN:

27590

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

7121

AN:

18620

East Asian (EAS)

AF:

0.227

AC:

8569

AN:

37778

South Asian (SAS)

AF:

0.247

AC:

15710

AN:

63590

European-Finnish (FIN)

AF:

0.342

AC:

13540

AN:

39570

Middle Eastern (MID)

AF:

0.287

AC:

1393

AN:

4860

European-Non Finnish (NFE)

AF:

0.391

AC:

335445

AN:

857948

Other (OTH)

AF:

0.341

AC:

16553

AN:

48558

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

12481

24962

37443

49924

62405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9800

19600

29400

39200

49000

<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:

0.280

AC:

42587

AN:

152146

Hom.:

7122

Cov.:

AF XY:

0.276

AC XY:

20497

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.108

AC:

4486

AN:

41532

American (AMR)

AF:

0.253

AC:

3870

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

1264

AN:

3466

East Asian (EAS)

AF:

0.231

AC:

1195

AN:

5172

South Asian (SAS)

AF:

0.249

AC:

1198

AN:

4814

European-Finnish (FIN)

AF:

0.318

AC:

3366

AN:

10578

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.386

AC:

26211

AN:

67976

Other (OTH)

AF:

0.299

AC:

633

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1488

2977

4465

5954

7442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.345

Hom.:

12208

Bravo

AF:

0.268

Asia WGS

AF:

0.260

AC:

904

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.6

(source)

DANN

Benign

0.66

PhyloP100

1.1

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over