rs1016807

Variant names:

• chr7-88896546-T-C
• rs1016807
• NM_181646.5:c.108+136462T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+136462T>C		intron_variant	Intron 1 of 3	ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+136462T>C		intron_variant	Intron 1 of 3	1	NM_181646.5	ENSP00000329638.4

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

African (AFR) AF: 0.757 AC: 31386 AN: 41436

American (AMR) AF: 0.461 AC: 7037 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3470

East Asian (EAS) AF: 0.581 AC: 2995 AN: 5158

South Asian (SAS) AF: 0.448 AC: 2158 AN: 4818

European-Finnish (FIN) AF: 0.350 AC: 3699 AN: 10566

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22054 AN: 67948

Other (OTH) AF: 0.492 AC: 1040 AN: 2112

Alfa AF: 0.394 Hom.: 4594

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
PhyloP100		-0.98
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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