ENST00000417927.1:n.2798-3954G>A

Variant names:

• chr4-122644147-G-A
• rs7685609
• ENST00000417927.1:n.2798-3954G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417927.1(IL21-AS1):​n.2798-3954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 152,204 control chromosomes in the GnomAD database, including 383 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 0.066 (383 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.2798-3954G>A		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2798-3954G>A		intron_variant	Intron 7 of 10	1

Frequencies

GnomAD3 genomes AF: 0.0655 AC: 9961 AN: 152086 Hom.: 380 Cov.: 32

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0655 AC: 9975 AN: 152204 Hom.: 383 Cov.: 32 AF XY: 0.0674 AC XY: 5017 AN XY: 74406

African (AFR) AF: 0.0385 AC: 1598 AN: 41520

American (AMR) AF: 0.116 AC: 1773 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3472

East Asian (EAS) AF: 0.0824 AC: 427 AN: 5182

South Asian (SAS) AF: 0.0721 AC: 347 AN: 4814

European-Finnish (FIN) AF: 0.0871 AC: 923 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4443 AN: 68020

Other (OTH) AF: 0.0815 AC: 172 AN: 2110

Alfa AF: 0.0568 Hom.: 193

Bravo AF: 0.0692

Asia WGS AF: 0.104 AC: 360 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	0.65
DANN	Benign	0.76
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7685609; hg19: chr4-123565302;