rs2126709

Variant names:

• chr11-123725219-C-T
• rs2126709
• NM_003455.4:c.*778G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003455.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF202	NM_003455.4	MANE Select	c.*778G>A		3_prime_UTR	Exon 9 of 9	NP_003446.2
	ZNF202	NM_001301779.2		c.*778G>A		3_prime_UTR	Exon 8 of 8	NP_001288708.1
	ZNF202	NM_001301780.2		c.*778G>A		3_prime_UTR	Exon 7 of 7	NP_001288709.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF202	ENST00000530393.6	TSL:1 MANE Select	c.*778G>A		3_prime_UTR	Exon 9 of 9	ENSP00000432504.1
	ZNF202	ENST00000336139.8	TSL:1	c.*778G>A		3_prime_UTR	Exon 8 of 8	ENSP00000337724.4
	ZNF202	ENST00000529691.1	TSL:2	c.*778G>A		3_prime_UTR	Exon 7 of 7	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0295 AC: 1226 AN: 41544

American (AMR) AF: 0.133 AC: 2033 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3466

East Asian (EAS) AF: 0.151 AC: 780 AN: 5174

South Asian (SAS) AF: 0.0270 AC: 130 AN: 4812

European-Finnish (FIN) AF: 0.0421 AC: 446 AN: 10592

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0173 AC: 1175 AN: 67994

Other (OTH) AF: 0.0431 AC: 91 AN: 2110

Alfa AF: 0.0304 Hom.: 620

Bravo AF: 0.0487

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.55
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2126709; hg19: chr11-123595927;