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GeneBe

rs1344706

Variant summary

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

The NM_194250.2(ZNF804A):c.256-19902A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151914 control chromosomes in the gnomAD Genomes database, including 8547 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 0.30 ( 8547 hom., cov: 32)

Consequence

ZNF804A
NM_194250.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.225

Links

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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=-0.91).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF804ANM_194250.2 linkuse as main transcriptc.256-19902A>C intron_variant ENST00000302277.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF804AENST00000302277.7 linkuse as main transcriptc.256-19902A>C intron_variant 1 NM_194250.2 P1

Frequencies

GnomAD3 genomes
AF:
0.304
AC:
46211
AN:
151914
Hom.:
8547
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0831
Gnomad AMI
AF:
0.386
Gnomad AMR
AF:
0.357
Gnomad ASJ
AF:
0.356
Gnomad EAS
AF:
0.499
Gnomad SAS
AF:
0.354
Gnomad FIN
AF:
0.405
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.389
Gnomad OTH
AF:
0.321
Alfa
AF:
0.376
Hom.:
20026
Bravo
AF:
0.294
Asia WGS
AF:
0.391
AC:
1363
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
6.9
Dann
Benign
0.76

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: rs1344706; hg19: chr2-185778428; API