NM_003455.4:c.-97-4244G>A

Variant names:

• chr11-123735229-C-T
• rs9326264
• NM_003455.4:c.-97-4244G>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.-97-4244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,974 control chromosomes in the GnomAD database, including 28,783 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 0.61 (28783 hom., cov: 31)
• Consequence: ZNF202 NM_003455.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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.-97-4244G>A		intron	N/A	NP_003446.2
	ZNF202	NM_001301779.2		c.-97-4244G>A		intron	N/A	NP_001288708.1
	ZNF202	NM_001301780.2		c.-97-4244G>A		intron	N/A	NP_001288709.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF202	ENST00000530393.6	TSL:1 MANE Select	c.-97-4244G>A		intron	N/A	ENSP00000432504.1
	ZNF202	ENST00000336139.8	TSL:1	c.-97-4244G>A		intron	N/A	ENSP00000337724.4
	ZNF202	ENST00000529691.1	TSL:2	c.-97-4244G>A		intron	N/A	ENSP00000433881.1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92875 AN: 151854 Hom.: 28775 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.611 AC: 92921 AN: 151974 Hom.: 28783 Cov.: 31 AF XY: 0.610 AC XY: 45277 AN XY: 74284

African (AFR) AF: 0.621 AC: 25740 AN: 41438

American (AMR) AF: 0.623 AC: 9525 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2331 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1824 AN: 5144

South Asian (SAS) AF: 0.557 AC: 2681 AN: 4812

European-Finnish (FIN) AF: 0.607 AC: 6406 AN: 10546

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42396 AN: 67968

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.624 Hom.: 80983

Bravo AF: 0.615

Asia WGS AF: 0.456 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.093
DANN	Benign	0.69
PhyloP100		-1.2
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: rs9326264; hg19: chr11-123605937;