Genetic Variant IL1F10:p.Ala51Asp (chr2-113074756-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_173161.3(IL1F10):c.152C>A(p.Ala51Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 1,611,940 control chromosomes in the GnomAD database, including 362,567 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36333 hom., cov: 32)

Exomes 𝑓: 0.67 ( 326234 hom. )

Consequence

IL1F10
NM_173161.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.13

Publications

64 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:

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 (MetaRNN=7.929842E-7).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1F10	NM_173161.3 link	c.152C>A	p.Ala51Asp	missense_variant	Exon 4 of 5	ENST00000341010.6	NP_775184.1
IL1F10	NM_032556.6 link	c.152C>A	p.Ala51Asp	missense_variant	Exon 3 of 4		NP_115945.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
IL1F10	ENST00000341010.6 link	c.152C>A	p.Ala51Asp	missense_variant	Exon 4 of 5	1	NM_173161.3	ENSP00000341794.2
IL1F10	ENST00000393197.3 link	c.152C>A	p.Ala51Asp	missense_variant	Exon 3 of 4	1		ENSP00000376893.2
IL1F10	ENST00000496265.1 link	n.218C>A		non_coding_transcript_exon_variant	Exon 1 of 2	1

Frequencies

GnomAD3 genomes

AF:

0.689

AC:

104642

AN:

151946

Hom.:

36282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.742

Gnomad AMI

AF:

0.741

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.711

Gnomad EAS

AF:

0.695

Gnomad SAS

AF:

0.782

Gnomad FIN

AF:

0.659

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.717

GnomAD2 exomes

AF:

0.695

AC:

174644

AN:

251366

AF XY:

0.697

show subpopulations

Gnomad AFR exome

AF:

0.745

Gnomad AMR exome

AF:

0.733

Gnomad ASJ exome

AF:

0.711

Gnomad EAS exome

AF:

0.696

Gnomad FIN exome

AF:

0.652

Gnomad NFE exome

AF:

0.655

Gnomad OTH exome

AF:

0.704

GnomAD4 exome

AF:

0.667

AC:

973100

AN:

1459876

Hom.:

326234

Cov.:

AF XY:

0.669

AC XY:

486182

AN XY:

726338

show subpopulations

African (AFR)

AF:

0.745

AC:

24921

AN:

33440

American (AMR)

AF:

0.729

AC:

32598

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.700

AC:

18285

AN:

26128

East Asian (EAS)

AF:

0.715

AC:

28396

AN:

39698

South Asian (SAS)

AF:

0.789

AC:

67996

AN:

86218

European-Finnish (FIN)

AF:

0.647

AC:

34566

AN:

53398

Middle Eastern (MID)

AF:

0.819

AC:

4700

AN:

5740

European-Non Finnish (NFE)

AF:

0.649

AC:

720626

AN:

1110214

Other (OTH)

AF:

0.680

AC:

41012

AN:

60320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

17969

35938

53908

71877

89846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19076

38152

57228

76304

95380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.689

AC:

104751

AN:

152064

Hom.:

36333

Cov.:

AF XY:

0.691

AC XY:

51340

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.742

AC:

30783

AN:

41474

American (AMR)

AF:

0.709

AC:

10831

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.711

AC:

2469

AN:

3472

East Asian (EAS)

AF:

0.694

AC:

3577

AN:

5156

South Asian (SAS)

AF:

0.783

AC:

3777

AN:

4822

European-Finnish (FIN)

AF:

0.659

AC:

6989

AN:

10600

Middle Eastern (MID)

AF:

0.840

AC:

247

AN:

294

European-Non Finnish (NFE)

AF:

0.646

AC:

43890

AN:

67950

Other (OTH)

AF:

0.719

AC:

1514

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1662

3325

4987

6650

8312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.669

Hom.:

84756

Bravo

AF:

0.697

TwinsUK

AF:

0.659

AC:

2442

ALSPAC

AF:

0.644

AC:

2481

ESP6500AA

AF:

0.729

AC:

3211

ESP6500EA

AF:

0.656

AC:

5640

ExAC

AF:

0.693

AC:

84139

Asia WGS

AF:

0.770

AC:

2678

AN:

3478

EpiCase

AF:

0.666

EpiControl

AF:

0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.040

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.45

DEOGEN2

Benign

0.0018

T;T

Eigen

Benign

-0.94

Eigen_PC

Benign

-0.65

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.10

.;T

MetaRNN

Benign

7.9e-7

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-2.5

N;N

PhyloP100

2.1

PrimateAI

Benign

0.41

PROVEAN

Benign

3.2

N;N

REVEL

Benign

0.034

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.057

MPC

0.043

ClinPred

0.0040

GERP RS

3.9

Varity_R

0.053

gMVP

0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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