chr16-3269193-C-T

Variant names:

• chr16-3269193-C-T
• rs224243
• ENST00000703449.1:c.-171+5310C>T

Variant summary

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

The ENST00000703449.1(ZNF263):​c.-171+5310C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,008 control chromosomes in the GnomAD database, including 22,552 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 0.53 (22552 hom., cov: 32)
• Consequence: ZNF263 ENST00000703449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 7 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]

LINC00921 (HGNC:26830): (long intergenic non-protein coding RNA 921)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF263	ENST00000703449.1	c.-171+5310C>T		intron_variant	Intron 1 of 1			ENSP00000515300.1
LINC00921	ENST00000706009.1	n.*42C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80257 AN: 151890 Hom.: 22506 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.529 AC: 80362 AN: 152008 Hom.: 22552 Cov.: 32 AF XY: 0.523 AC XY: 38872 AN XY: 74282

African (AFR) AF: 0.727 AC: 30127 AN: 41466

American (AMR) AF: 0.521 AC: 7953 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1499 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1631 AN: 5178

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4824

European-Finnish (FIN) AF: 0.447 AC: 4702 AN: 10526

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31411 AN: 67966

Other (OTH) AF: 0.500 AC: 1057 AN: 2112

Alfa AF: 0.488 Hom.: 7875

Bravo AF: 0.545

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.85
DANN	Benign	0.57
PhyloP100		-2.0
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: rs224243; hg19: chr16-3319193;