rs6959888

Variant names:

• chr7-88967071-A-G
• rs6959888
• NM_181646.5:c.108+206987A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181646.5(ZNF804B):​c.108+206987A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,396 control chromosomes in the GnomAD database, including 947 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 0.11 (947 hom., cov: 31)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+206987A>G		intron_variant	Intron 1 of 3	ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+206987A>G		intron_variant	Intron 1 of 3	1	NM_181646.5	ENSP00000329638.4

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16132 AN: 151280 Hom.: 948 Cov.: 31

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.107 AC: 16134 AN: 151396 Hom.: 947 Cov.: 31 AF XY: 0.109 AC XY: 8062 AN XY: 73940

African (AFR) AF: 0.0676 AC: 2798 AN: 41398

American (AMR) AF: 0.125 AC: 1899 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 473 AN: 3454

East Asian (EAS) AF: 0.185 AC: 939 AN: 5064

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4808

European-Finnish (FIN) AF: 0.0976 AC: 1030 AN: 10556

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7621 AN: 67650

Other (OTH) AF: 0.118 AC: 248 AN: 2102

Alfa AF: 0.113 Hom.: 3269

Bravo AF: 0.107

Asia WGS AF: 0.194 AC: 672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		1.0
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

Other links and lift over

dbSNP: rs6959888; hg19: chr7-88596385;