rs148065820

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_001129996.2(ZNF222):​c.474G>A​(p.Gln158Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

ZNF222
NM_001129996.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.935
Variant links:
Genes affected
ZNF222 (HGNC:13015): (zinc finger protein 222) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP7
Synonymous conserved (PhyloP=-0.935 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF222NM_001129996.2 linkc.474G>A p.Gln158Gln synonymous_variant Exon 4 of 4 ENST00000391960.4 NP_001123468.1 Q9UK12-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF222ENST00000391960.4 linkc.474G>A p.Gln158Gln synonymous_variant Exon 4 of 4 1 NM_001129996.2 ENSP00000375822.2 Q9UK12-2
ZNF222ENST00000187879.12 linkc.354G>A p.Gln118Gln synonymous_variant Exon 4 of 4 1 ENSP00000187879.6 Q9UK12-1
ENSG00000267022ENST00000591793.1 linkn.262+4538G>A intron_variant Intron 3 of 10 2 ENSP00000467018.1 K7ENM7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.15
DANN
Benign
0.39
PhyloP100
-0.94

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.15
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs148065820; hg19: chr19-44536181; API