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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053042.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF518B	NM_053042.3	MANE Select	c.*78G>A	3_prime_UTR	Exon 3 of 3	NP_444270.2
ZNF518B	NM_001375816.1		c.*78G>A	3_prime_UTR	Exon 3 of 3	NP_001362745.1
ZNF518B	NM_001375817.1		c.*78G>A	3_prime_UTR	Exon 2 of 2	NP_001362746.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF518B	ENST00000326756.4	TSL:3 MANE Select	c.*78G>A	3_prime_UTR	Exon 3 of 3	ENSP00000317614.3
ZNF518B	ENST00000908724.1		c.*78G>A	3_prime_UTR	Exon 4 of 4	ENSP00000578783.1
ZNF518B	ENST00000908725.1		c.*78G>A	3_prime_UTR	Exon 4 of 4	ENSP00000578784.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over