chr2-184937190-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_194250.2(ZNF804A):ā€‹c.1794A>Gā€‹(p.Lys598=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,595,064 control chromosomes in the GnomAD database, including 33,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: š‘“ 0.15 ( 2259 hom., cov: 33)
Exomes š‘“: 0.20 ( 30930 hom. )

Consequence

ZNF804A
NM_194250.2 synonymous

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.00
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 2-184937190-A-G is Benign according to our data. Variant chr2-184937190-A-G is described in ClinVar as [Benign]. Clinvar id is 3060253.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=2 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF804ANM_194250.2 linkuse as main transcriptc.1794A>G p.Lys598= synonymous_variant 4/4 ENST00000302277.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF804AENST00000302277.7 linkuse as main transcriptc.1794A>G p.Lys598= synonymous_variant 4/41 NM_194250.2 P1

Frequencies

GnomAD3 genomes
AF:
0.153
AC:
23262
AN:
152064
Hom.:
2256
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0360
Gnomad AMI
AF:
0.247
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.208
Gnomad EAS
AF:
0.227
Gnomad SAS
AF:
0.258
Gnomad FIN
AF:
0.215
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.201
Gnomad OTH
AF:
0.173
GnomAD3 exomes
AF:
0.197
AC:
45328
AN:
230060
Hom.:
5072
AF XY:
0.206
AC XY:
25895
AN XY:
125492
show subpopulations
Gnomad AFR exome
AF:
0.0343
Gnomad AMR exome
AF:
0.107
Gnomad ASJ exome
AF:
0.207
Gnomad EAS exome
AF:
0.245
Gnomad SAS exome
AF:
0.280
Gnomad FIN exome
AF:
0.232
Gnomad NFE exome
AF:
0.207
Gnomad OTH exome
AF:
0.214
GnomAD4 exome
AF:
0.201
AC:
290554
AN:
1442882
Hom.:
30930
Cov.:
47
AF XY:
0.205
AC XY:
146779
AN XY:
717646
show subpopulations
Gnomad4 AFR exome
AF:
0.0295
Gnomad4 AMR exome
AF:
0.109
Gnomad4 ASJ exome
AF:
0.205
Gnomad4 EAS exome
AF:
0.236
Gnomad4 SAS exome
AF:
0.274
Gnomad4 FIN exome
AF:
0.231
Gnomad4 NFE exome
AF:
0.202
Gnomad4 OTH exome
AF:
0.196
GnomAD4 genome
AF:
0.153
AC:
23257
AN:
152182
Hom.:
2259
Cov.:
33
AF XY:
0.153
AC XY:
11406
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0359
Gnomad4 AMR
AF:
0.135
Gnomad4 ASJ
AF:
0.208
Gnomad4 EAS
AF:
0.227
Gnomad4 SAS
AF:
0.260
Gnomad4 FIN
AF:
0.215
Gnomad4 NFE
AF:
0.201
Gnomad4 OTH
AF:
0.170
Alfa
AF:
0.182
Hom.:
1398
Bravo
AF:
0.142
Asia WGS
AF:
0.232
AC:
805
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

ZNF804A-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesNov 12, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
CADD
Benign
5.1
DANN
Benign
0.60

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs728534; hg19: chr2-185801917; COSMIC: COSV56436034; API