rs2137497

Variant names:

• chr4-122637099-T-G
• rs2137497
• ENST00000417927.1:n.2797+8103T>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+8103T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,994 control chromosomes in the GnomAD database, including 18,061 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 0.47 (18061 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 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+8103T>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+8103T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71026 AN: 151878 Hom.: 18063 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.467 AC: 71038 AN: 151994 Hom.: 18061 Cov.: 32 AF XY: 0.461 AC XY: 34266 AN XY: 74306

African (AFR) AF: 0.299 AC: 12393 AN: 41434

American (AMR) AF: 0.383 AC: 5850 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2031 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1373 AN: 5166

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4824

European-Finnish (FIN) AF: 0.569 AC: 6017 AN: 10566

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40138 AN: 67946

Other (OTH) AF: 0.475 AC: 1004 AN: 2112

Alfa AF: 0.527 Hom.: 47498

Bravo AF: 0.448

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.71
PhyloP100		-1.2

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: rs2137497;

hg19: chr4-123558254;