rs10248351

chr7-88852128-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+92044T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 152,062 control chromosomes in the GnomAD database, including 439 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 0.045 (439 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804B	NM_181646.5	c.108+92044T>C		intron_variant		ENST00000333190.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+92044T>C		intron_variant		1	NM_181646.5	P1

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6760 AN: 151944 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00503

Gnomad OTH AF: 0.0418

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

GnomAD4 genome AF: 0.0447 AC: 6793 AN: 152062 Hom.: 439 Cov.: 32 AF XY: 0.0432 AC XY: 3209 AN XY: 74348

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0228

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.0208

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00503

Gnomad4 OTH AF: 0.0423

Alfa AF: 0.0108 Hom.: 67

Bravo AF: 0.0510

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	7.2
Dann	Benign	0.79

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: rs10248351; hg19: chr7-88481442;