chr10-45055302-T-C

Variant names:

• chr10-45055302-T-C
• rs7905526
• ENST00000456938.7:n.476+10225A>G

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+10225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,178 control chromosomes in the GnomAD database, including 39,818 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 0.72 (39818 hom., cov: 33)
• Consequence: ZNF22-AS1 ENST00000456938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 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.476+10225A>G		intron_variant	Intron 5 of 6	1
ZNF22-AS1	ENST00000598522.5	n.764+10225A>G		intron_variant	Intron 4 of 4	5
ZNF22-AS1	ENST00000599308.3	n.765-39134A>G		intron_variant	Intron 7 of 7	5

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109885 AN: 152060 Hom.: 39795 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.723 AC: 109957 AN: 152178 Hom.: 39818 Cov.: 33 AF XY: 0.724 AC XY: 53864 AN XY: 74388

African (AFR) AF: 0.743 AC: 30834 AN: 41518

American (AMR) AF: 0.746 AC: 11409 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3466

East Asian (EAS) AF: 0.509 AC: 2638 AN: 5180

South Asian (SAS) AF: 0.722 AC: 3484 AN: 4826

European-Finnish (FIN) AF: 0.746 AC: 7888 AN: 10576

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49204 AN: 68000

Other (OTH) AF: 0.720 AC: 1520 AN: 2112

Alfa AF: 0.718 Hom.: 101632

Bravo AF: 0.724

Asia WGS AF: 0.673 AC: 2338 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	1.9
DANN	Benign	0.48
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7905526; hg19: chr10-45550750;