rs16868596

Positions:

• chr7-89034948-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_181646.5(ZNF804B):​c.109-183207G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0191 in 152,130 control chromosomes in the GnomAD database, including 36 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 0.019 (36 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0191 (2907/152130) while in subpopulation SAS AF= 0.0311 (150/4818). AF 95% confidence interval is 0.0285. There are 36 homozygotes in gnomad4. There are 1447 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.109-183207G>T		intron_variant		ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.109-183207G>T		intron_variant		1	NM_181646.5	ENSP00000329638.4

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 2902 AN: 152014 Hom.: 36 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.00925

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0259

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

GnomAD4 genome AF: 0.0191 AC: 2907 AN: 152130 Hom.: 36 Cov.: 32 AF XY: 0.0195 AC XY: 1447 AN XY: 74376

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.0221

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.00925

Gnomad4 NFE AF: 0.0113

Gnomad4 OTH AF: 0.0256

Alfa AF: 0.0153 Hom.: 4

Bravo AF: 0.0208

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.35

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: rs16868596; hg19: chr7-88664262;