Genetic Variant ZNF808:n.*745G>T (chr19-52563640-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000487863.5(ZNF808):n.*745G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 153,258 control chromosomes in the GnomAD database, including 8,906 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 0.33 ( 8877 hom., cov: 33)

Exomes 𝑓: 0.21 ( 29 hom. )

Consequence

ZNF808
ENST00000487863.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.708

Publications

4 publications found

Variant links:

Genes affected

ZNF808 (HGNC:33230): (zinc finger protein 808) 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]

ZNF808 links:

ZNF701 (HGNC:25597): (zinc finger protein 701) Predicted to enable DNA-binding transcription factor 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]

ZNF701 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487863.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF808	ENST00000487863.5	TSL:1	n.*745G>T	non_coding_transcript_exon	Exon 4 of 4	ENSP00000420522.1	Q8N4W9-2
ZNF808	ENST00000487863.5	TSL:1	n.*745G>T	3_prime_UTR	Exon 4 of 4	ENSP00000420522.1	Q8N4W9-2
ZNF701	ENST00000478039.1	TSL:4	n.230-6400G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50615

AN:

151964

Hom.:

8871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.414

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.0511

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.319

GnomAD4 exome

AF:

0.212

AC:

249

AN:

1174

Hom.:

Cov.:

AF XY:

0.188

AC XY:

116

AN XY:

618

show subpopulations

African (AFR)

AF:

0.400

AC:

AN:

American (AMR)

AF:

0.176

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.159

AC:

AN:

138

European-Finnish (FIN)

AF:

0.237

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.224

AC:

192

AN:

858

Other (OTH)

AF:

0.191

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

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:

0.333

AC:

50653

AN:

152084

Hom.:

8877

Cov.:

AF XY:

0.329

AC XY:

24435

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.414

AC:

17163

AN:

41462

American (AMR)

AF:

0.339

AC:

5178

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

1080

AN:

3468

East Asian (EAS)

AF:

0.0512

AC:

265

AN:

5180

South Asian (SAS)

AF:

0.209

AC:

1007

AN:

4828

European-Finnish (FIN)

AF:

0.312

AC:

3299

AN:

10578

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.317

AC:

21571

AN:

67980

Other (OTH)

AF:

0.315

AC:

666

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1726

3452

5177

6903

8629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.328

Hom.:

2006

Bravo

AF:

0.342

Asia WGS

AF:

0.152

AC:

529

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

(source)

DANN

Benign

0.63

PhyloP100

0.71

Splicing

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