rs190081

Variant names:

• chr16-3273569-A-G
• rs190081
• ENST00000703449.1:c.-171+9686A>G

Variant summary

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

The ENST00000703449.1(ZNF263):​c.-171+9686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,156 control chromosomes in the GnomAD database, including 3,586 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 0.19 (3585 hom., cov: 31)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ZNF263 ENST00000703449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 15 publications found

Genes affected

ZNF263 (HGNC:13056): (zinc finger protein 263) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000279330 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703449.1. 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
	ZNF263	ENST00000703449.1		c.-171+9686A>G		intron	N/A	ENSP00000515300.1
	ENSG00000279330	ENST00000622989.1	TSL:6	n.-40A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29544 AN: 152018 Hom.: 3586 Cov.: 31

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.250 AC: 5 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.286 AC: 4 AN: 14

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.194 AC: 29539 AN: 152136 Hom.: 3585 Cov.: 31 AF XY: 0.196 AC XY: 14610 AN XY: 74352

African (AFR) AF: 0.0681 AC: 2830 AN: 41530

American (AMR) AF: 0.289 AC: 4411 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3472

East Asian (EAS) AF: 0.0378 AC: 196 AN: 5184

South Asian (SAS) AF: 0.109 AC: 526 AN: 4830

European-Finnish (FIN) AF: 0.293 AC: 3097 AN: 10554

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16995 AN: 67980

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.238 Hom.: 7645

Bravo AF: 0.192

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.69
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs190081; hg19: chr16-3323569;