Variant rs11471 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006963.5(ZNF22):c.*308T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 247,318 control chromosomes in the GnomAD database, including 71,604 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 0.76 ( 44457 hom., cov: 32)

Exomes 𝑓: 0.75 ( 27147 hom. )

Consequence

ZNF22
NM_006963.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

ZNF22 (HGNC:13012): (zinc finger protein 22) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF22 links:

CEP164P1 (HGNC:44988): (centrosomal protein 164 pseudogene 1)

CEP164P1 links:

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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF22	NM_006963.5 link	c.*308T>C		3_prime_UTR_variant	2/2	ENST00000298299.4	NP_008894.2	P17026A0A024R7T4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF22	ENST00000298299.4 link	c.*308T>C		3_prime_UTR_variant	2/2	1	NM_006963.5	ENSP00000298299.3		P17026
CEP164P1	ENST00000456938.6 link	n.619-276A>G		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.764

AC:

116128

AN:

152018

Hom.:

44420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.781

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.789

Gnomad ASJ

AF:

0.673

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.750

Gnomad FIN

AF:

0.788

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.765

Gnomad OTH

AF:

0.751

GnomAD4 exome

AF:

0.753

AC:

71666

AN:

95182

Hom.:

27147

Cov.:

AF XY:

0.753

AC XY:

36220

AN XY:

48104

show subpopulations

Gnomad4 AFR exome

AF:

0.802

Gnomad4 AMR exome

AF:

0.790

Gnomad4 ASJ exome

AF:

0.684

Gnomad4 EAS exome

AF:

0.571

Gnomad4 SAS exome

AF:

0.746

Gnomad4 FIN exome

AF:

0.785

Gnomad4 NFE exome

AF:

0.761

Gnomad4 OTH exome

AF:

0.757

GnomAD4 genome

AF:

0.764

AC:

116222

AN:

152136

Hom.:

44457

Cov.:

AF XY:

0.766

AC XY:

56939

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.781

Gnomad4 AMR

AF:

0.789

Gnomad4 ASJ

AF:

0.673

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.748

Gnomad4 FIN

AF:

0.788

Gnomad4 NFE

AF:

0.764

Gnomad4 OTH

AF:

0.754

Alfa

AF:

0.757

Hom.:

58852

Bravo

AF:

0.765

Asia WGS

AF:

0.725

AC:

2519

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.5

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over