rs2390352

Variant names:

• chr4-122637175-C-T
• rs2390352
• ENST00000417927.1:n.2797+8179C>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.2797+8179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,216 control chromosomes in the GnomAD database, including 54,831 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 0.82 (54831 hom., cov: 33)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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+8179C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2797+8179C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124987 AN: 152098 Hom.: 54819 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.821 AC: 125038 AN: 152216 Hom.: 54831 Cov.: 33 AF XY: 0.828 AC XY: 61616 AN XY: 74434

African (AFR) AF: 0.478 AC: 19810 AN: 41468

American (AMR) AF: 0.923 AC: 14118 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3388 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5181 AN: 5190

South Asian (SAS) AF: 0.951 AC: 4587 AN: 4822

European-Finnish (FIN) AF: 0.966 AC: 10259 AN: 10620

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64698 AN: 68030

Other (OTH) AF: 0.862 AC: 1823 AN: 2116

Alfa AF: 0.914 Hom.: 125037

Bravo AF: 0.804

Asia WGS AF: 0.925 AC: 3216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		0.055

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: rs2390352;

hg19: chr4-123558330;