7-88776732-T-C

Position:

• chr7-88776732-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+16648T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 150,780 control chromosomes in the GnomAD database, including 366 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 0.049 (366 hom., cov: 26)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+16648T>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.108+16648T>C		intron_variant		1	NM_181646.5	ENSP00000329638	P1

Frequencies

GnomAD3 genomes AF: 0.0494 AC: 7438 AN: 150662 Hom.: 366 Cov.: 26

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0486

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

GnomAD4 genome AF: 0.0493 AC: 7437 AN: 150780 Hom.: 366 Cov.: 26 AF XY: 0.0517 AC XY: 3807 AN XY: 73572

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.0455

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0486

Alfa AF: 0.0384 Hom.: 22

Bravo AF: 0.0573

Asia WGS AF: 0.153 AC: 531 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.8
DANN	Benign	0.74

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: rs4727180; hg19: chr7-88406046;