19-52563640-G-T

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

2

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]
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]

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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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF808XR_002958314.2 linkn.3622G>T non_coding_transcript_exon_variant Exon 6 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF808ENST00000487863.5 linkn.*745G>T non_coding_transcript_exon_variant Exon 4 of 4 1 ENSP00000420522.1 Q8N4W9-2
ZNF808ENST00000487863.5 linkn.*745G>T 3_prime_UTR_variant Exon 4 of 4 1 ENSP00000420522.1 Q8N4W9-2
ZNF701ENST00000478039.1 linkn.230-6400G>T intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.333
AC:
50615
AN:
151964
Hom.:
8871
Cov.:
33
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.:
29
Cov.:
0
AF XY:
0.188
AC XY:
116
AN XY:
618
show subpopulations
African (AFR)
AF:
0.400
AC:
4
AN:
10
American (AMR)
AF:
0.176
AC:
6
AN:
34
Ashkenazi Jewish (ASJ)
AF:
0.250
AC:
3
AN:
12
East Asian (EAS)
AF:
0.00
AC:
0
AN:
14
South Asian (SAS)
AF:
0.159
AC:
22
AN:
138
European-Finnish (FIN)
AF:
0.237
AC:
9
AN:
38
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
0.224
AC:
192
AN:
858
Other (OTH)
AF:
0.191
AC:
13
AN:
68
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
9
18
26
35
44
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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.:
33
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
0
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
0
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.4
DANN
Benign
0.63
PhyloP100
0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12327640; hg19: chr19-53066893; API