rs2285444

Positions:

• chr7-88797522-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+37438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 152,228 control chromosomes in the GnomAD database, including 532 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 0.060 (532 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF804B	NM_181646.5	c.108+37438C>T		intron_variant		ENST00000333190.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+37438C>T		intron_variant		1	NM_181646.5	P1

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9170 AN: 152110 Hom.: 531 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0603 AC: 9176 AN: 152228 Hom.: 532 Cov.: 32 AF XY: 0.0627 AC XY: 4664 AN XY: 74430

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0302 Hom.: 316

Bravo AF: 0.0683

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2285444; hg19: chr7-88426836; COSMIC: COSV51880097; COSMIC: COSV51880097;