rs3491

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF706	ENST00000520984.5	c.*13-4703T>C		intron_variant		5		ENSP00000427761.1
ZNF706	ENST00000518071.5	n.*58-4703T>C		intron_variant		4		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

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.329

Alfa AF: 0.282 Hom.: 3036

Bravo AF: 0.351

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.68

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: rs3491; hg19: chr8-102195318;