rs1023564

Positions:

• chr7-89212400-A-C
• chr7-89212400-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181646.5(ZNF804B):​c.109-5755A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,800 control chromosomes in the GnomAD database, including 26,811 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 0.59 (26811 hom., cov: 31)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.109-5755A>C		intron_variant		ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.109-5755A>C		intron_variant		1	NM_181646.5	ENSP00000329638.4

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89292 AN: 151682 Hom.: 26782 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.589 AC: 89375 AN: 151800 Hom.: 26811 Cov.: 31 AF XY: 0.586 AC XY: 43429 AN XY: 74172

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.566

Alfa AF: 0.506 Hom.: 1835

Bravo AF: 0.585

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.69

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

Other links and lift over

dbSNP: rs1023564; hg19: chr7-88841714;