rs2893008

Variant names:

• chr4-122631659-A-G
• rs2893008
• ENST00000417927.1:n.2797+2663A>G

Variant summary

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

The ENST00000417927.1(IL21-AS1):​n.2797+2663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 152,236 control chromosomes in the GnomAD database, including 283 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 0.051 (283 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0735 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	NR_104126.1		n.2797+2663A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2797+2663A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7702 AN: 152118 Hom.: 283 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0475

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

GnomAD4 genome AF: 0.0506 AC: 7696 AN: 152236 Hom.: 283 Cov.: 32 AF XY: 0.0511 AC XY: 3805 AN XY: 74420

African (AFR) AF: 0.0106 AC: 439 AN: 41568

American (AMR) AF: 0.0399 AC: 609 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4826

European-Finnish (FIN) AF: 0.0981 AC: 1040 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5118 AN: 67998

Other (OTH) AF: 0.0460 AC: 97 AN: 2108

Alfa AF: 0.0655 Hom.: 647

Bravo AF: 0.0439

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.72
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2893008;

hg19: chr4-123552814;