20-53567166-C-T

Position:

• chr20-53567166-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.*2122G>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 0.0869 in 152,232 control chromosomes in the GnomAD database, including 741 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 0.087 (735 hom., cov: 33)
  • Exomes 𝑓: 0.15 (6 hom.)
• Consequence: ZNF217 NM_006526.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.790

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• 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.*2122G>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.*2122G>A		3_prime_UTR_variant	6/6	5	NM_006526.3	ENSP00000360526.2
ZNF217	ENST00000302342	c.*2122G>A		3_prime_UTR_variant	5/5	1		ENSP00000304308.3
ENSG00000197670	ENST00000424252.2	n.556-3106C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13163 AN: 151710 Hom.: 734 Cov.: 33

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0853

GnomAD4 exome AF: 0.149 AC: 60 AN: 404 Hom.: 6 Cov.: 0 AF XY: 0.164 AC XY: 41 AN XY: 250

Gnomad4 FIN exome AF: 0.148

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.0868 AC: 13173 AN: 151828 Hom.: 735 Cov.: 33 AF XY: 0.0850 AC XY: 6307 AN XY: 74198

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.0821

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0403

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.113 Hom.: 194

Bravo AF: 0.0795

Asia WGS AF: 0.0300 AC: 103 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	11
DANN	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1056948; hg19: chr20-52183705;