10-45052620-A-G

Variant names:

• chr10-45052620-A-G
• rs1936396
• ENST00000456938.7:n.476+12907T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456938.7(ZNF22-AS1):​n.476+12907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,084 control chromosomes in the GnomAD database, including 45,700 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 0.77 (45700 hom., cov: 32)
• Consequence: ZNF22-AS1 ENST00000456938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

ZNF22-AS1 (HGNC:23509): (ZNF22 antisense RNA 1) Predicted to be located in extracellular region. [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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456938.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF22-AS1	ENST00000456938.7	TSL:1	n.476+12907T>C		intron	N/A
	ZNF22-AS1	ENST00000598522.5	TSL:5	n.764+12907T>C		intron	N/A
	ZNF22-AS1	ENST00000599308.3	TSL:5	n.765-36452T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117657 AN: 151966 Hom.: 45665 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.774 AC: 117746 AN: 152084 Hom.: 45700 Cov.: 32 AF XY: 0.775 AC XY: 57590 AN XY: 74316

African (AFR) AF: 0.809 AC: 33591 AN: 41520

American (AMR) AF: 0.774 AC: 11827 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2341 AN: 3468

East Asian (EAS) AF: 0.591 AC: 3061 AN: 5178

South Asian (SAS) AF: 0.750 AC: 3615 AN: 4822

European-Finnish (FIN) AF: 0.790 AC: 8349 AN: 10570

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52601 AN: 67934

Other (OTH) AF: 0.761 AC: 1608 AN: 2114

Alfa AF: 0.766 Hom.: 69327

Bravo AF: 0.775

Asia WGS AF: 0.737 AC: 2559 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1936396; hg19: chr10-45548068; COSMIC: COSV71791018;