dbSNP rs10487035: ZNF804B:c.108+5485C>G (chr7-88765569-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_181646.5(ZNF804B):c.108+5485C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 151,700 control chromosomes in the GnomAD database, including 566 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 0.070 ( 566 hom., cov: 33)

Consequence

ZNF804B
NM_181646.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0750

Publications

0 publications found

Variant links:

Genes affected

ZNF804B (HGNC:21958): (zinc finger protein 804B) Predicted to enable metal ion binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF804B links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_181646.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181646.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF804B	NM_181646.5	MANE Select	c.108+5485C>G		intron	N/A	NP_857597.1	A4D1E1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF804B	ENST00000333190.5	TSL:1 MANE Select	c.108+5485C>G		intron	N/A	ENSP00000329638.4	A4D1E1

Frequencies

GnomAD3 genomes

AF:

0.0701

AC:

10633

AN:

151582

Hom.:

565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0876

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.0473

Gnomad FIN

AF:

0.0484

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0388

Gnomad OTH

AF:

0.0656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0701

AC:

10636

AN:

151700

Hom.:

566

Cov.:

AF XY:

0.0733

AC XY:

5436

AN XY:

74142

show subpopulations

African (AFR)

AF:

0.0875

AC:

3601

AN:

41170

American (AMR)

AF:

0.127

AC:

1933

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0274

AC:

AN:

3462

East Asian (EAS)

AF:

0.279

AC:

1441

AN:

5156

South Asian (SAS)

AF:

0.0471

AC:

227

AN:

4820

European-Finnish (FIN)

AF:

0.0484

AC:

511

AN:

10564

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0388

AC:

2637

AN:

67962

Other (OTH)

AF:

0.0659

AC:

139

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

487

975

1462

1950

2437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0137

Hom.:

Bravo

AF:

0.0786

Asia WGS

AF:

0.157

AC:

545

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.075

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over