rs7694252

chr4-122640281-G-Achr4-122640281-G-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.2798-7820G>A 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 0.748 in 152,034 control chromosomes in the GnomAD database, including 42,867 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 0.75 (42867 hom., cov: 31)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.2798-7820G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2798-7820G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113625 AN: 151916 Hom.: 42815 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.748 AC: 113737 AN: 152034 Hom.: 42867 Cov.: 31 AF XY: 0.758 AC XY: 56299 AN XY: 74320

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.753

Alfa AF: 0.715 Hom.: 6486

Bravo AF: 0.748

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.2
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7694252; hg19: chr4-123561436;