chr20-53567963-C-T

Position:

• chr20-53567963-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006526.3(ZNF217):​c.*1325G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 152,556 control chromosomes in the GnomAD database, including 748 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 0.086 (743 hom., cov: 32)
  • Exomes 𝑓: 0.14 (5 hom.)
• Consequence: ZNF217 NM_006526.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

Genes affected

ZNF217 (HGNC:13009): (zinc finger protein 217) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in mitochondrion and nuclear speck. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000197670 (HGNC:56842): (ZNF217 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF217	NM_006526.3	c.*1325G>A		3_prime_UTR_variant	6/6	ENST00000371471.7	NP_006517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF217	ENST00000371471	c.*1325G>A		3_prime_UTR_variant	6/6	5	NM_006526.3	ENSP00000360526.2
ZNF217	ENST00000302342	c.*1325G>A		3_prime_UTR_variant	5/5	1		ENSP00000304308.3
ENSG00000197670	ENST00000424252.2	n.556-2309C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13080 AN: 152016 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0843

GnomAD4 exome AF: 0.140 AC: 59 AN: 422 Hom.: 5 Cov.: 0 AF XY: 0.154 AC XY: 39 AN XY: 254

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.0860 AC: 13079 AN: 152134 Hom.: 743 Cov.: 32 AF XY: 0.0843 AC XY: 6271 AN XY: 74378

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0834

Alfa AF: 0.114 Hom.: 1400

Bravo AF: 0.0787

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.54

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: rs2766671; hg19: chr20-52184502;