Genetic Variant ENST00000417927.1:n.2798-5137T>C (chr4-122642964-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.2798-5137T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,082 control chromosomes in the GnomAD database, including 32,299 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 0.65 ( 32299 hom., cov: 32)

Consequence

IL21-AS1
ENST00000417927.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839

Publications

9 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=-0.97).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1 link	n.2798-5137T>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.2798-5137T>C		intron_variant	Intron 7 of 10	1

Frequencies

GnomAD3 genomes

AF:

0.649

AC:

98671

AN:

151964

Hom.:

32276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.706

Gnomad AMR

AF:

0.686

Gnomad ASJ

AF:

0.668

Gnomad EAS

AF:

0.771

Gnomad SAS

AF:

0.773

Gnomad FIN

AF:

0.734

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.675

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

GnomAD4 genome

AF:

0.649

AC:

98729

AN:

152082

Hom.:

32299

Cov.:

AF XY:

0.659

AC XY:

48957

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.613

AC:

25403

AN:

41468

American (AMR)

AF:

0.686

AC:

10486

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.668

AC:

2315

AN:

3468

East Asian (EAS)

AF:

0.771

AC:

3985

AN:

5168

South Asian (SAS)

AF:

0.772

AC:

3721

AN:

4820

European-Finnish (FIN)

AF:

0.734

AC:

7754

AN:

10566

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.629

AC:

42767

AN:

67990

Other (OTH)

AF:

0.678

AC:

1431

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1775

3549

5324

7098

8873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.634

Hom.:

65190

Bravo

AF:

0.642

Asia WGS

AF:

0.735

AC:

2554

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.42

(source)

DANN

Benign

0.72

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