chr19-52562408-A-G

Variant names:

• chr19-52562408-A-G
• rs12985487
• ENST00000487863.5:n.*423-910A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000487863.5(ZNF808):​n.*423-910A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,178 control chromosomes in the GnomAD database, including 271 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 0.058 (271 hom., cov: 32)
• Consequence: ZNF808 ENST00000487863.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 4 publications found

Genes affected

ZNF808 (HGNC:33230): (zinc finger protein 808) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF701 (HGNC:25597): (zinc finger protein 701) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487863.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF808	ENST00000487863.5	TSL:1	n.*423-910A>G		intron	N/A	ENSP00000420522.1	Q8N4W9-2
	ZNF701	ENST00000478039.1	TSL:4	n.229+6358A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0578 AC: 8793 AN: 152062 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0578 AC: 8794 AN: 152178 Hom.: 271 Cov.: 32 AF XY: 0.0581 AC XY: 4320 AN XY: 74400

African (AFR) AF: 0.0463 AC: 1922 AN: 41526

American (AMR) AF: 0.0579 AC: 885 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4830

European-Finnish (FIN) AF: 0.0910 AC: 963 AN: 10578

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0645 AC: 4386 AN: 68008

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0643 Hom.: 530

Bravo AF: 0.0553

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.34
PhyloP100		-0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12985487; hg19: chr19-53065661;