rs926716

Positions:

• chr20-18292988-G-C
• chr20-18292988-G-T

Variant summary

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

The NM_001352452.2(ZNF133):​c.-432+4384G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,150 control chromosomes in the GnomAD database, including 8,153 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 0.32 (8153 hom., cov: 32)
• Consequence: ZNF133 NM_001352452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.924

Genes affected

ZNF133 (HGNC:12917): (zinc finger protein 133) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF133	NM_001352452.2	c.-432+4384G>C		intron_variant		ENST00000425686.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF133	ENST00000425686.3	c.-432+4384G>C		intron_variant		3	NM_001352452.2	A2
	ENST00000666293.1	n.426-2959C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48494 AN: 152032 Hom.: 8154 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.319 AC: 48501 AN: 152150 Hom.: 8153 Cov.: 32 AF XY: 0.316 AC XY: 23511 AN XY: 74398

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.321

Alfa AF: 0.224 Hom.: 500

Bravo AF: 0.314

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	13
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs926716; hg19: chr20-18273632;