7-88776732-T-C

Variant names:

• chr7-88776732-T-C
• rs4727180
• NM_181646.5:c.108+16648T>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+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
• Publications: 2 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=-0.78).
• 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 rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+16648T>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+16648T>C		intron_variant	Intron 1 of 3	1	NM_181646.5	ENSP00000329638.4

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

African (AFR) AF: 0.0277 AC: 1143 AN: 41252

American (AMR) AF: 0.109 AC: 1627 AN: 14974

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1319 AN: 4934

South Asian (SAS) AF: 0.0455 AC: 216 AN: 4748

European-Finnish (FIN) AF: 0.0390 AC: 401 AN: 10284

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2533 AN: 67820

Other (OTH) AF: 0.0486 AC: 102 AN: 2100

Alfa AF: 0.0382 Hom.: 23

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
PhyloP100		0.33
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: rs4727180; hg19: chr7-88406046;