rs2893008

Positions:

• chr4-122631659-A-G

Variant summary

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

The NR_104126.1(IL21-AS1):​n.2797+2663A>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 0.0506 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 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.2797+2663A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2797+2663A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0399

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0460

Alfa AF: 0.0680 Hom.: 550

Bravo AF: 0.0439

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2893008; hg19: chr4-123552814;