11-123725219-C-T

Position:

• chr11-123725219-C-T

Variant summary

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

The NM_003455.4(ZNF202):​c.*778G>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 0.0392 in 152,172 control chromosomes in the GnomAD database, including 274 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 0.039 (274 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF202 NM_003455.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF202	NM_003455.4	c.*778G>A		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	c.*778G>A		3_prime_UTR_variant	9/9	1	NM_003455.4	ENSP00000432504.1
ZNF202	ENST00000336139	c.*778G>A		3_prime_UTR_variant	8/8	1		ENSP00000337724.4
ZNF202	ENST00000529691	c.*778G>A		3_prime_UTR_variant	7/7	2		ENSP00000433881.1

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5958 AN: 152054 Hom.: 274 Cov.: 33

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0436

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0392 AC: 5970 AN: 152172 Hom.: 274 Cov.: 33 AF XY: 0.0443 AC XY: 3294 AN XY: 74396

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0308 Hom.: 286

Bravo AF: 0.0487

Asia WGS AF: 0.0920 AC: 319 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	0.13
DANN	Benign	0.55

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: rs2126709; hg19: chr11-123595927;