Genetic Variant IL1F10:p.Asp24Asp (chr2-113074368-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_173161.3(IL1F10):c.72T>C(p.Asp24Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 1,613,220 control chromosomes in the GnomAD database, including 12,868 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 0.093 ( 1260 hom., cov: 32)

Exomes 𝑓: 0.092 ( 11608 hom. )

Consequence

IL1F10
NM_173161.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

21 publications found

Variant links:

Genes affected

IL1F10 (HGNC:15552): (interleukin 1 family member 10) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. This cytokine is thought to participate in a network of interleukin 1 family members to regulate adapted and innate immune responses. Two alternatively spliced transcript variants encoding the same protein have been reported. [provided by RefSeq, Jul 2008]

IL1F10 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP7

Synonymous conserved (PhyloP=-1.04 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1F10	NM_173161.3 link	c.72T>C	p.Asp24Asp	synonymous_variant	Exon 3 of 5	ENST00000341010.6	NP_775184.1	Q8WWZ1-1
IL1F10	NM_032556.6 link	c.72T>C	p.Asp24Asp	synonymous_variant	Exon 2 of 4		NP_115945.4	Q8WWZ1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL1F10	ENST00000341010.6 link	c.72T>C	p.Asp24Asp	synonymous_variant	Exon 3 of 5	1	NM_173161.3	ENSP00000341794.2	Q8WWZ1-1
IL1F10	ENST00000393197.3 link	c.72T>C	p.Asp24Asp	synonymous_variant	Exon 2 of 4	1		ENSP00000376893.2	Q8WWZ1-1
IL1F10	ENST00000496265.1 link	n.-171T>C		upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0934

AC:

14209

AN:

152154

Hom.:

1267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0556

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.537

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.0934

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0704

Gnomad OTH

AF:

0.109

GnomAD2 exomes

AF:

0.129

AC:

32401

AN:

251306

AF XY:

0.125

show subpopulations

Gnomad AFR exome

AF:

0.0536

Gnomad AMR exome

AF:

0.165

Gnomad ASJ exome

AF:

0.144

Gnomad EAS exome

AF:

0.551

Gnomad FIN exome

AF:

0.0911

Gnomad NFE exome

AF:

0.0729

Gnomad OTH exome

AF:

0.123

GnomAD4 exome

AF:

0.0924

AC:

135017

AN:

1460948

Hom.:

11608

Cov.:

AF XY:

0.0925

AC XY:

67234

AN XY:

726814

show subpopulations

African (AFR)

AF:

0.0515

AC:

1722

AN:

33464

American (AMR)

AF:

0.161

AC:

7182

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

3646

AN:

26122

East Asian (EAS)

AF:

0.567

AC:

22518

AN:

39684

South Asian (SAS)

AF:

0.106

AC:

9107

AN:

86218

European-Finnish (FIN)

AF:

0.0901

AC:

4812

AN:

53414

Middle Eastern (MID)

AF:

0.122

AC:

701

AN:

5756

European-Non Finnish (NFE)

AF:

0.0708

AC:

78651

AN:

1111216

Other (OTH)

AF:

0.111

AC:

6678

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

5324

10648

15971

21295

26619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0933

AC:

14210

AN:

152272

Hom.:

1260

Cov.:

AF XY:

0.0990

AC XY:

7371

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0556

AC:

2312

AN:

41560

American (AMR)

AF:

0.127

AC:

1941

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

486

AN:

3472

East Asian (EAS)

AF:

0.537

AC:

2776

AN:

5172

South Asian (SAS)

AF:

0.127

AC:

611

AN:

4816

European-Finnish (FIN)

AF:

0.0934

AC:

991

AN:

10612

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0704

AC:

4789

AN:

68022

Other (OTH)

AF:

0.107

AC:

227

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

616

1232

1847

2463

3079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0762

Hom.:

254

Bravo

AF:

0.0987

Asia WGS

AF:

0.293

AC:

1020

AN:

3478

EpiCase

AF:

0.0758

EpiControl

AF:

0.0807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.086

(source)

DANN

Benign

0.26

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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2-113074368-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over