Genetic Variant ZNF518B:c.*1303C>T (chr4-10441801-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_053042.3(ZNF518B):c.*1303C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,252 control chromosomes in the GnomAD database, including 3,897 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 0.22 ( 3896 hom., cov: 33)

Exomes 𝑓: 0.31 ( 1 hom. )

Consequence

ZNF518B
NM_053042.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206

Publications

6 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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 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.*1303C>T	3_prime_UTR	Exon 3 of 3	NP_444270.2
ZNF518B	NM_001375816.1		c.*1303C>T	3_prime_UTR	Exon 3 of 3	NP_001362745.1
ZNF518B	NM_001375817.1		c.*1303C>T	3_prime_UTR	Exon 2 of 2	NP_001362746.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF518B	ENST00000326756.4	TSL:3 MANE Select	c.*1303C>T		3_prime_UTR	Exon 3 of 3	ENSP00000317614.3

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32859

AN:

152092

Hom.:

3899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.213

GnomAD4 exome

AF:

0.310

AC:

AN:

Hom.:

Cov.:

AF XY:

0.281

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.289

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.216

AC:

32861

AN:

152210

Hom.:

3896

Cov.:

AF XY:

0.219

AC XY:

16320

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.114

AC:

4718

AN:

41532

American (AMR)

AF:

0.275

AC:

4202

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

897

AN:

3472

East Asian (EAS)

AF:

0.193

AC:

1002

AN:

5180

South Asian (SAS)

AF:

0.232

AC:

1120

AN:

4828

European-Finnish (FIN)

AF:

0.306

AC:

3234

AN:

10582

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

17018

AN:

68006

Other (OTH)

AF:

0.210

AC:

444

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1358

2715

4073

5430

6788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.241

Hom.:

3373

Bravo

AF:

0.210

Asia WGS

AF:

0.196

AC:

681

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.4

(source)

DANN

Benign

0.30

PhyloP100

-0.21

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