rs13393273

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_194250.2(ZNF804A):​c.111+13880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,068 control chromosomes in the GnomAD database, including 12,468 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 0.40 ( 12468 hom., cov: 33)

Consequence

ZNF804A
NM_194250.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.541
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF804ANM_194250.2 linkuse as main transcriptc.111+13880A>G intron_variant ENST00000302277.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF804AENST00000302277.7 linkuse as main transcriptc.111+13880A>G intron_variant 1 NM_194250.2 P1

Frequencies

GnomAD3 genomes
AF:
0.399
AC:
60660
AN:
151950
Hom.:
12455
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.455
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.296
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.163
Gnomad SAS
AF:
0.394
Gnomad FIN
AF:
0.394
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.406
Gnomad OTH
AF:
0.402
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.399
AC:
60707
AN:
152068
Hom.:
12468
Cov.:
33
AF XY:
0.396
AC XY:
29443
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.455
Gnomad4 AMR
AF:
0.296
Gnomad4 ASJ
AF:
0.408
Gnomad4 EAS
AF:
0.163
Gnomad4 SAS
AF:
0.396
Gnomad4 FIN
AF:
0.394
Gnomad4 NFE
AF:
0.406
Gnomad4 OTH
AF:
0.399
Alfa
AF:
0.417
Hom.:
1700
Bravo
AF:
0.391
Asia WGS
AF:
0.269
AC:
937
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.99
DANN
Benign
0.62

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: rs13393273; hg19: chr2-185477677; API