rs7694252

Variant names:

• chr4-122640281-G-A
• rs7694252
• ENST00000417927.1:n.2798-7820G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-122640281-G-A
• chr4-122640281-G-T

Variant summary

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

The ENST00000417927.1(IL21-AS1):​n.2798-7820G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,034 control chromosomes in the GnomAD database, including 42,867 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 0.75 (42867 hom., cov: 31)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 3 publications found

Genes affected

IL21-AS1 (HGNC:40299): (IL21 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	NR_104126.1		n.2798-7820G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2798-7820G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113625 AN: 151916 Hom.: 42815 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.748 AC: 113737 AN: 152034 Hom.: 42867 Cov.: 31 AF XY: 0.758 AC XY: 56299 AN XY: 74320

African (AFR) AF: 0.783 AC: 32456 AN: 41462

American (AMR) AF: 0.801 AC: 12223 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4227 AN: 5160

South Asian (SAS) AF: 0.841 AC: 4048 AN: 4814

European-Finnish (FIN) AF: 0.815 AC: 8623 AN: 10578

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47111 AN: 67976

Other (OTH) AF: 0.753 AC: 1587 AN: 2108

Alfa AF: 0.724 Hom.: 13260

Bravo AF: 0.748

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7694252; hg19: chr4-123561436;