rs1398553

Variant names:

• chr4-122626913-A-G
• rs1398553
• ENST00000417927.1:n.2685+100A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-122626913-A-G
• chr4-122626913-A-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.2685+100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 153,034 control chromosomes in the GnomAD database, including 46,289 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 0.77 (46084 hom., cov: 32)
  • Exomes 𝑓: 0.67 (205 hom.)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 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.2685+100A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2685+100A>G		intron	N/A
	IL21-AS1	ENST00000668520.1		n.915A>G		non_coding_transcript_exon	Exon 7 of 7

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116917 AN: 152034 Hom.: 46022 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.778

GnomAD4 exome AF: 0.669 AC: 590 AN: 882 Hom.: 205 AF XY: 0.635 AC XY: 311 AN XY: 490

African (AFR) AF: 1.00 AC: 10 AN: 10

American (AMR) AF: 0.700 AC: 7 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 16 AN: 24

East Asian (EAS) AF: 0.963 AC: 77 AN: 80

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.453 AC: 58 AN: 128

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.663 AC: 390 AN: 588

Other (OTH) AF: 0.750 AC: 30 AN: 40

GnomAD4 genome AF: 0.769 AC: 117042 AN: 152152 Hom.: 46084 Cov.: 32 AF XY: 0.767 AC XY: 57031 AN XY: 74366

African (AFR) AF: 0.921 AC: 38269 AN: 41532

American (AMR) AF: 0.815 AC: 12453 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4585 AN: 5166

South Asian (SAS) AF: 0.859 AC: 4136 AN: 4814

European-Finnish (FIN) AF: 0.554 AC: 5857 AN: 10580

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46492 AN: 67984

Other (OTH) AF: 0.778 AC: 1645 AN: 2114

Alfa AF: 0.726 Hom.: 24089

Bravo AF: 0.794

Asia WGS AF: 0.885 AC: 3076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.56
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs1398553; hg19: chr4-123548068;