Genetic Variant IL21-AS1:n.2798-4798T>C (chr4-122643303-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000417927.1(IL21-AS1):n.2798-4798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,012 control chromosomes in the GnomAD database, including 17,512 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 ( 17512 hom., cov: 32)

Consequence

IL21-AS1
ENST00000417927.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.838

Publications

8 publications found

Variant links:

Genes affected

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

IL21-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1 link	n.2798-4798T>C		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1 link	n.2798-4798T>C		intron_variant	Intron 7 of 10	1

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72447

AN:

151896

Hom.:

17517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.502

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.589

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.471

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

GnomAD4 genome

AF:

0.477

AC:

72457

AN:

152012

Hom.:

17512

Cov.:

AF XY:

0.481

AC XY:

35715

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.393

AC:

16273

AN:

41452

American (AMR)

AF:

0.473

AC:

7227

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.514

AC:

1784

AN:

3472

East Asian (EAS)

AF:

0.503

AC:

2597

AN:

5168

South Asian (SAS)

AF:

0.475

AC:

2285

AN:

4812

European-Finnish (FIN)

AF:

0.589

AC:

6223

AN:

10568

Middle Eastern (MID)

AF:

0.497

AC:

146

AN:

294

European-Non Finnish (NFE)

AF:

0.507

AC:

34475

AN:

67950

Other (OTH)

AF:

0.473

AC:

1000

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1897

3794

5690

7587

9484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.492

Hom.:

35104

Bravo

AF:

0.466

Asia WGS

AF:

0.452

AC:

1570

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.3

(source)

DANN

Benign

0.53

PhyloP100

0.84

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over