rs10487035

chr7-88765569-C-Gchr7-88765569-C-T

Variant summary

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

The NM_181646.5(ZNF804B):c.108+5485C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 151,700 control chromosomes in the GnomAD database, including 566 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 0.070 (566 hom., cov: 33)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804B	NM_181646.5	c.108+5485C>G		intron_variant		ENST00000333190.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+5485C>G		intron_variant		1	NM_181646.5	P1

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10633 AN: 151582 Hom.: 565 Cov.: 33

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0701 AC: 10636 AN: 151700 Hom.: 566 Cov.: 33 AF XY: 0.0733 AC XY: 5436 AN XY: 74142

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.0471

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0388

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0137 Hom.: 1

Bravo AF: 0.0786

Asia WGS AF: 0.157 AC: 545 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	10
Dann	Benign	0.56

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: rs10487035; hg19: chr7-88394883;