10-45021899-C-T

Variant names:

• chr10-45021899-C-T
• rs2018728
• ENST00000456938.7:n.477-5731G>A

Variant summary

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

The ENST00000456938.7(ZNF22-AS1):​n.477-5731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,000 control chromosomes in the GnomAD database, including 23,318 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 0.53 (23318 hom., cov: 32)
• Consequence: ZNF22-AS1 ENST00000456938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF22-AS1	ENST00000456938.7	n.477-5731G>A		intron_variant	Intron 5 of 6	1
ZNF22-AS1	ENST00000598522.5	n.765-5731G>A		intron_variant	Intron 4 of 4	5
ZNF22-AS1	ENST00000599308.3	n.765-5731G>A		intron_variant	Intron 7 of 7	5

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79939 AN: 151882 Hom.: 23312 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.526 AC: 79962 AN: 152000 Hom.: 23318 Cov.: 32 AF XY: 0.527 AC XY: 39168 AN XY: 74262

African (AFR) AF: 0.287 AC: 11895 AN: 41448

American (AMR) AF: 0.574 AC: 8771 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2027 AN: 3464

East Asian (EAS) AF: 0.199 AC: 1027 AN: 5160

South Asian (SAS) AF: 0.524 AC: 2521 AN: 4814

European-Finnish (FIN) AF: 0.682 AC: 7200 AN: 10554

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44729 AN: 67968

Other (OTH) AF: 0.560 AC: 1181 AN: 2108

Alfa AF: 0.601 Hom.: 14747

Bravo AF: 0.507

Asia WGS AF: 0.401 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2018728; hg19: chr10-45517347;