dbSNP rs16347: IL1A:c.*925_*928dupTTCA (chr2-112774138-T-TTGAA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000575.5(IL1A):c.*925_*928dupTTCA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.69 ( 36882 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

IL1A
NM_000575.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.453

Publications

4 publications found

Variant links:

Genes affected

IL1A (HGNC:5991): (interleukin 1 alpha) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This cytokine is a pleiotropic cytokine involved in various immune responses, inflammatory processes, and hematopoiesis. This cytokine is produced by monocytes and macrophages as a proprotein, which is proteolytically processed and released in response to cell injury, and thus induces apoptosis. This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. It has been suggested that the polymorphism of these genes is associated with rheumatoid arthritis and Alzheimer's disease. [provided by RefSeq, Jul 2008]

IL1A links:

ENSG00000299339 (HGNC:):

ENSG00000299339 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 2-112774138-T-TTGAA is Benign according to our data. Variant chr2-112774138-T-TTGAA is described in ClinVar as Benign. ClinVar VariationId is 1245422.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000575.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1A	NM_000575.5	MANE Select	c.925_928dupTTCA		3_prime_UTR	Exon 7 of 7	NP_000566.3
	IL1A	NM_001371554.1		c.925_928dupTTCA		3_prime_UTR	Exon 7 of 7	NP_001358483.1	P01583

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL1A	ENST00000263339.4	TSL:1 MANE Select	c.925_928dupTTCA	3_prime_UTR	Exon 7 of 7	ENSP00000263339.3	P01583
IL1A	ENST00000959423.1		c.925_928dupTTCA	3_prime_UTR	Exon 6 of 6	ENSP00000629482.1
ENSG00000299339	ENST00000762706.1		n.404+3243_404+3246dupTGAA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104575

AN:

151464

Hom.:

36843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.779

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.294

Gnomad SAS

AF:

0.696

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.698

Gnomad OTH

AF:

0.682

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.690

AC:

104655

AN:

151582

Hom.:

36882

Cov.:

AF XY:

0.682

AC XY:

50488

AN XY:

74060

show subpopulations

African (AFR)

AF:

0.779

AC:

32189

AN:

41318

American (AMR)

AF:

0.602

AC:

9165

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.732

AC:

2535

AN:

3462

East Asian (EAS)

AF:

0.293

AC:

1517

AN:

5172

South Asian (SAS)

AF:

0.696

AC:

3353

AN:

4818

European-Finnish (FIN)

AF:

0.594

AC:

6208

AN:

10454

Middle Eastern (MID)

AF:

0.789

AC:

232

AN:

294

European-Non Finnish (NFE)

AF:

0.698

AC:

47331

AN:

67824

Other (OTH)

AF:

0.677

AC:

1425

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1587

3174

4760

6347

7934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<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:

0.695

Hom.:

3978

Bravo

AF:

0.687

Asia WGS

AF:

0.522

AC:

1818

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over