rs1398553

chr4-122626913-A-Gchr4-122626913-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104126.1(IL21-AS1):n.2685+100A>G variant causes a intron, non coding transcript 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 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.2685+100A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2685+100A>G		intron_variant, non_coding_transcript_variant		1
IL21-AS1	ENST00000668520.1	n.915A>G		non_coding_transcript_exon_variant	7/7

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.700

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.963

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.453

Gnomad4 NFE exome AF: 0.663

Gnomad4 OTH exome AF: 0.750

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

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.778

Alfa AF: 0.719 Hom.: 20213

Bravo AF: 0.794

Asia WGS AF: 0.885 AC: 3076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.1
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398553; hg19: chr4-123548068;