rs1016807

chr7-88896546-T-C

Variant summary

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

The NM_181646.5(ZNF804B):c.108+136462T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,986 control chromosomes in the GnomAD database, including 19,771 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 0.47 (19771 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804B	NM_181646.5	c.108+136462T>C		intron_variant		ENST00000333190.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+136462T>C		intron_variant		1	NM_181646.5	P1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72087 AN: 151870 Hom.: 19732 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.475 AC: 72184 AN: 151986 Hom.: 19771 Cov.: 32 AF XY: 0.476 AC XY: 35390 AN XY: 74272

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.492

Alfa AF: 0.383 Hom.: 2515

Bravo AF: 0.496

Asia WGS AF: 0.550 AC: 1909 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.75

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: rs1016807; hg19: chr7-88525860; COSMIC: COSV60842839;