rs13137822

chr4-122636081-C-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+7085C>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 0.48 in 152,012 control chromosomes in the GnomAD database, including 18,608 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 0.48 (18608 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.2797+7085C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2797+7085C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72969 AN: 151894 Hom.: 18599 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.480 AC: 73013 AN: 152012 Hom.: 18608 Cov.: 32 AF XY: 0.481 AC XY: 35769 AN XY: 74298

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.500

Alfa AF: 0.521 Hom.: 2648

Bravo AF: 0.471

Asia WGS AF: 0.589 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.35
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13137822; hg19: chr4-123557236;