rs1856591

Variant names:

• chr10-45103170-C-T
• rs1856591
• ENST00000448600.5:n.570-2671G>A

Variant summary

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

The ENST00000448600.5(ZNF22-AS1):​n.570-2671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,968 control chromosomes in the GnomAD database, including 19,778 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 0.51 (19778 hom., cov: 32)
• Consequence: ZNF22-AS1 ENST00000448600.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 5 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]

RSU1P2 (HGNC:44391): (Ras suppressor protein 1 pseudogene 2)

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 = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1P2	NR_024472.1	n.821-2671G>A		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF22-AS1	ENST00000448600.5	n.570-2671G>A		intron_variant	Intron 6 of 6	1
ZNF22-AS1	ENST00000619977.1	n.821-2671G>A		intron_variant	Intron 8 of 8	1
ZNF22-AS1	ENST00000423875.1	n.1374-2671G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76931 AN: 151850 Hom.: 19764 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.507 AC: 76988 AN: 151968 Hom.: 19778 Cov.: 32 AF XY: 0.511 AC XY: 37926 AN XY: 74288

African (AFR) AF: 0.452 AC: 18735 AN: 41442

American (AMR) AF: 0.590 AC: 9016 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1643 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2689 AN: 5160

South Asian (SAS) AF: 0.418 AC: 2010 AN: 4814

European-Finnish (FIN) AF: 0.566 AC: 5975 AN: 10548

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35402 AN: 67948

Other (OTH) AF: 0.490 AC: 1034 AN: 2112

Alfa AF: 0.516 Hom.: 64197

Bravo AF: 0.510

Asia WGS AF: 0.445 AC: 1547 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	1.1
DANN	Benign	0.47
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1856591; hg19: chr10-45598618;