ENST00000456938.7:n.477-1069G>C

Variant names:

• chr10-45017237-C-G
• rs7077596
• ENST00000456938.7:n.477-1069G>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.477-1069G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,052 control chromosomes in the GnomAD database, including 20,676 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 0.49 (20676 hom., cov: 32)
• Consequence: ZNF22-AS1 ENST00000456938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 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.477-1069G>C		intron	N/A
	ZNF22-AS1	ENST00000598522.5	TSL:5	n.765-1069G>C		intron	N/A
	ZNF22-AS1	ENST00000599308.3	TSL:5	n.765-1069G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74665 AN: 151934 Hom.: 20674 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.491 AC: 74671 AN: 152052 Hom.: 20676 Cov.: 32 AF XY: 0.494 AC XY: 36713 AN XY: 74322

African (AFR) AF: 0.244 AC: 10133 AN: 41462

American (AMR) AF: 0.541 AC: 8273 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1892 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5176

South Asian (SAS) AF: 0.514 AC: 2472 AN: 4812

European-Finnish (FIN) AF: 0.660 AC: 6972 AN: 10570

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42304 AN: 67966

Other (OTH) AF: 0.510 AC: 1078 AN: 2112

Alfa AF: 0.545 Hom.: 3017

Bravo AF: 0.471

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.6
DANN	Benign	0.77
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7077596; hg19: chr10-45512685;