chr10-45004773-A-G

Position:

• chr10-45004773-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006963.5(ZNF22):​c.*730A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 166,938 control chromosomes in the GnomAD database, including 5,225 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 0.20 (5198 hom., cov: 32)
  • Exomes 𝑓: 0.061 (27 hom.)
• Consequence: ZNF22 NM_006963.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88

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]

CEP164P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF22	NM_006963.5	c.*730A>G		3_prime_UTR_variant	2/2	ENST00000298299.4	NP_008894.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF22	ENST00000298299.4	c.*730A>G		3_prime_UTR_variant	2/2	1	NM_006963.5	ENSP00000298299.3
CEP164P1	ENST00000456938.6	n.619-698T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29649 AN: 151932 Hom.: 5177 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.0611 AC: 909 AN: 14888 Hom.: 27 Cov.: 0 AF XY: 0.0601 AC XY: 425 AN XY: 7068

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0608

Gnomad4 NFE exome AF: 0.0698

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.195 AC: 29712 AN: 152050 Hom.: 5198 Cov.: 32 AF XY: 0.196 AC XY: 14543 AN XY: 74310

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0523

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0586

Gnomad4 OTH AF: 0.160

Alfa AF: 0.102 Hom.: 2055

Bravo AF: 0.219

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.39
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs11494; hg19: chr10-45500221;