rs3183878

Positions:

• chr11-123725995-A-C
• chr11-123725995-A-T

Variant summary

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

The NM_003455.4(ZNF202):​c.*2T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,606,222 control chromosomes in the GnomAD database, including 122,328 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 0.41 (13035 hom., cov: 32)
  • Exomes 𝑓: 0.38 (109293 hom.)
• Consequence: ZNF202 NM_003455.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

Genes affected

ZNF202 (HGNC:12994): (zinc finger protein 202) 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 chromosome; nuclear body; and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF202	NM_003455.4	c.*2T>G		3_prime_UTR_variant	9/9	ENST00000530393.6	NP_003446.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF202	ENST00000530393.6	c.*2T>G		3_prime_UTR_variant	9/9	1	NM_003455.4	ENSP00000432504.1
ZNF202	ENST00000336139.8	c.*2T>G		3_prime_UTR_variant	8/8	1		ENSP00000337724.4
ZNF202	ENST00000529691.1	c.*2T>G		3_prime_UTR_variant	7/7	2		ENSP00000433881.1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62005 AN: 151824 Hom.: 13035 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.415

GnomAD3 exomes AF: 0.365 AC: 89896 AN: 246386 Hom.: 17205 AF XY: 0.365 AC XY: 48576 AN XY: 132952

Gnomad AFR exome AF: 0.489

Gnomad AMR exome AF: 0.317

Gnomad ASJ exome AF: 0.360

Gnomad EAS exome AF: 0.168

Gnomad SAS exome AF: 0.316

Gnomad FIN exome AF: 0.386

Gnomad NFE exome AF: 0.402

Gnomad OTH exome AF: 0.395

GnomAD4 exome AF: 0.384 AC: 558692 AN: 1454282 Hom.: 109293 Cov.: 48 AF XY: 0.382 AC XY: 276212 AN XY: 722512

Gnomad4 AFR exome AF: 0.505

Gnomad4 AMR exome AF: 0.323

Gnomad4 ASJ exome AF: 0.367

Gnomad4 EAS exome AF: 0.197

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.381

Gnomad4 NFE exome AF: 0.395

Gnomad4 OTH exome AF: 0.383

GnomAD4 genome AF: 0.408 AC: 62034 AN: 151940 Hom.: 13035 Cov.: 32 AF XY: 0.402 AC XY: 29838 AN XY: 74260

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.411

Alfa AF: 0.407 Hom.: 15132

Bravo AF: 0.410

Asia WGS AF: 0.257 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.91
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3183878; hg19: chr11-123596703;