11-123735229-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF202NM_003455.4 linkuse as main transcriptc.-97-4244G>A intron_variant ENST00000530393.6 NP_003446.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF202ENST00000530393.6 linkuse as main transcriptc.-97-4244G>A intron_variant 1 NM_003455.4 ENSP00000432504 P1O95125-1

Frequencies

GnomAD3 genomes
AF:
0.612
AC:
92875
AN:
151854
Hom.:
28775
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.621
Gnomad4 AMR
AF:
0.623
Gnomad4 ASJ
AF:
0.671
Gnomad4 EAS
AF:
0.355
Gnomad4 SAS
AF:
0.557
Gnomad4 FIN
AF:
0.607
Gnomad4 NFE
AF:
0.624
Gnomad4 OTH
AF:
0.633
Alfa
AF:
0.624
Hom.:
50100
Bravo
AF:
0.615
Asia WGS
AF:
0.456
AC:
1588
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.093
DANN
Benign
0.69

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9326264; hg19: chr11-123605937; API