NM_194250.2:c.112-25240T>C

Variant summary

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

The NM_194250.2(ZNF804A):​c.112-25240T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,932 control chromosomes in the GnomAD database, including 10,564 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 0.32 ( 10564 hom., cov: 32)

Consequence

ZNF804A
NM_194250.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.156

Publications

6 publications found
Variant links:
Genes affected
ZNF804A (HGNC:21711): (zinc finger protein 804A) The protein encoded by this gene is a zinc finger binding protein. Polymorphisms in this gene, especially rs1344706, are thought to confer increased susceptibility to schizophrenia, bipolar disorder, and heroin addiciton. [provided by RefSeq, Nov 2015]
ZNF804A Gene-Disease associations (from GenCC):
  • complex neurodevelopmental disorder
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF804ANM_194250.2 linkc.112-25240T>C intron_variant Intron 1 of 3 ENST00000302277.7 NP_919226.1 Q7Z570

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF804AENST00000302277.7 linkc.112-25240T>C intron_variant Intron 1 of 3 1 NM_194250.2 ENSP00000303252.6 Q7Z570
ENSG00000299447ENST00000763602.1 linkn.51-753A>G intron_variant Intron 1 of 2
ENSG00000299447ENST00000763603.1 linkn.72-753A>G intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.320
AC:
48548
AN:
151812
Hom.:
10527
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.618
Gnomad AMI
AF:
0.194
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.0434
Gnomad SAS
AF:
0.144
Gnomad FIN
AF:
0.130
Gnomad MID
AF:
0.357
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.320
AC:
48633
AN:
151932
Hom.:
10564
Cov.:
32
AF XY:
0.311
AC XY:
23080
AN XY:
74260
show subpopulations
African (AFR)
AF:
0.619
AC:
25607
AN:
41362
American (AMR)
AF:
0.210
AC:
3196
AN:
15246
Ashkenazi Jewish (ASJ)
AF:
0.288
AC:
998
AN:
3466
East Asian (EAS)
AF:
0.0433
AC:
224
AN:
5170
South Asian (SAS)
AF:
0.143
AC:
688
AN:
4820
European-Finnish (FIN)
AF:
0.130
AC:
1373
AN:
10592
Middle Eastern (MID)
AF:
0.377
AC:
110
AN:
292
European-Non Finnish (NFE)
AF:
0.230
AC:
15619
AN:
67956
Other (OTH)
AF:
0.303
AC:
641
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1400
2800
4200
5600
7000
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
434
868
1302
1736
2170
<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:
0.264
Hom.:
860
Bravo
AF:
0.339
Asia WGS
AF:
0.133
AC:
463
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.0
DANN
Benign
0.38
PhyloP100
-0.16
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs7605689; hg19: chr2-185705856; COSMIC: COSV107394095; API