rs2285444

Variant names:

• chr7-88797522-C-T
• rs2285444
• NM_181646.5:c.108+37438C>T

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+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
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+37438C>T		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+37438C>T		intron_variant	Intron 1 of 3	1	NM_181646.5	ENSP00000329638.4

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

African (AFR) AF: 0.108 AC: 4479 AN: 41530

American (AMR) AF: 0.0856 AC: 1308 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3472

East Asian (EAS) AF: 0.278 AC: 1440 AN: 5172

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4826

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10626

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0215 AC: 1463 AN: 68004

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0356 Hom.: 998

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
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2285444; hg19: chr7-88426836; COSMIC: COSV51880097; COSMIC: COSV51880097;