7-89065756-A-T

Position:

• chr7-89065756-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.109-152399A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,764 control chromosomes in the GnomAD database, including 11,057 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 0.36 (11057 hom., cov: 31)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.109-152399A>T		intron_variant		ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.109-152399A>T		intron_variant		1	NM_181646.5	ENSP00000329638.4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54917 AN: 151646 Hom.: 11010 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.363 AC: 55026 AN: 151764 Hom.: 11057 Cov.: 31 AF XY: 0.367 AC XY: 27186 AN XY: 74150

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.341

Alfa AF: 0.313 Hom.: 1030

Bravo AF: 0.375

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.035
DANN	Benign	0.48

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: rs10236237; hg19: chr7-88695070;