rs3491

Variant names:

• chr8-101183090-A-G
• rs3491
• ENST00000520984.5:c.*13-4703T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-101183090-A-G
• chr8-101183090-A-T

Variant summary

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

The ENST00000520984.5(ZNF706):​c.*13-4703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,542 control chromosomes in the GnomAD database, including 9,999 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 0.34 (9999 hom., cov: 28)
• Consequence: ZNF706 ENST00000520984.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 5 publications found

Genes affected

ZNF706 (HGNC:24992): (zinc finger protein 706) Predicted to enable metal ion binding activity. Predicted to be involved in negative regulation of stem cell population maintenance and negative regulation of transcription, DNA-templated. Predicted to be located in cytoplasm and 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520984.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF706	ENST00000520984.5	TSL:5	c.*13-4703T>C		intron	N/A	ENSP00000427761.1
	ZNF706	ENST00000518071.5	TSL:4	n.*58-4703T>C		intron	N/A	ENSP00000431059.1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 51937 AN: 151426 Hom.: 9987 Cov.: 28

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.343 AC: 51982 AN: 151542 Hom.: 9999 Cov.: 28 AF XY: 0.343 AC XY: 25404 AN XY: 74040

African (AFR) AF: 0.517 AC: 21322 AN: 41228

American (AMR) AF: 0.352 AC: 5365 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1148 AN: 5138

South Asian (SAS) AF: 0.360 AC: 1724 AN: 4794

European-Finnish (FIN) AF: 0.289 AC: 3028 AN: 10478

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17735 AN: 67900

Other (OTH) AF: 0.329 AC: 691 AN: 2102

Alfa AF: 0.282 Hom.: 3405

Bravo AF: 0.351

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		-0.054
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: rs3491; hg19: chr8-102195318;