rs717474

Variant names:

• chr7-89161983-G-A
• rs717474
• NM_181646.5:c.109-56172G>A

Variant summary

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

The NM_181646.5(ZNF804B):​c.109-56172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,944 control chromosomes in the GnomAD database, including 13,253 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 0.41 (13253 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.109-56172G>A		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.109-56172G>A		intron_variant	Intron 1 of 3	1	NM_181646.5	ENSP00000329638.4

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62057 AN: 151824 Hom.: 13245 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.409 AC: 62085 AN: 151944 Hom.: 13253 Cov.: 32 AF XY: 0.408 AC XY: 30293 AN XY: 74228

African (AFR) AF: 0.333 AC: 13784 AN: 41446

American (AMR) AF: 0.347 AC: 5288 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3470

East Asian (EAS) AF: 0.169 AC: 873 AN: 5174

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4820

European-Finnish (FIN) AF: 0.465 AC: 4905 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32182 AN: 67930

Other (OTH) AF: 0.435 AC: 918 AN: 2110

Alfa AF: 0.424 Hom.: 4749

Bravo AF: 0.392

Asia WGS AF: 0.360 AC: 1255 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.10
PhyloP100		-0.27
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: rs717474; hg19: chr7-88791297;