Variant rs6761276 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173161.3(IL1F10):c.131T>C(p.Ile44Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,610,742 control chromosomes in the GnomAD database, including 267,979 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.57 ( 24932 hom., cov: 33)

Exomes 𝑓: 0.57 ( 243047 hom. )

Consequence

IL1F10
NM_173161.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.5109908E-6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1F10	NM_173161.3 linkuse as main transcript	c.131T>C	p.Ile44Thr	missense_variant	4/5	ENST00000341010.6	NP_775184.1
IL1F10	NM_032556.6 linkuse as main transcript	c.131T>C	p.Ile44Thr	missense_variant	3/4		NP_115945.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1F10	ENST00000341010.6 linkuse as main transcript	c.131T>C	p.Ile44Thr	missense_variant	4/5	1	NM_173161.3	ENSP00000341794	P1	Q8WWZ1-1
IL1F10	ENST00000393197.3 linkuse as main transcript	c.131T>C	p.Ile44Thr	missense_variant	3/4	1		ENSP00000376893	P1	Q8WWZ1-1
IL1F10	ENST00000496265.1 linkuse as main transcript	n.197T>C		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

86156

AN:

152026

Hom.:

24901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.585

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.576

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.655

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.575

Gnomad OTH

AF:

0.581

GnomAD3 exomes

AF:

0.560

AC:

140726

AN:

251370

Hom.:

41199

AF XY:

0.569

AC XY:

77247

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.585

Gnomad AMR exome

AF:

0.563

Gnomad ASJ exome

AF:

0.570

Gnomad EAS exome

AF:

0.170

Gnomad SAS exome

AF:

0.689

Gnomad FIN exome

AF:

0.552

Gnomad NFE exome

AF:

0.583

Gnomad OTH exome

AF:

0.574

GnomAD4 exome

AF:

0.571

AC:

833354

AN:

1458598

Hom.:

243047

Cov.:

AF XY:

0.575

AC XY:

417007

AN XY:

725772

show subpopulations

Gnomad4 AFR exome

AF:

0.584

Gnomad4 AMR exome

AF:

0.564

Gnomad4 ASJ exome

AF:

0.564

Gnomad4 EAS exome

AF:

0.148

Gnomad4 SAS exome

AF:

0.684

Gnomad4 FIN exome

AF:

0.548

Gnomad4 NFE exome

AF:

0.579

Gnomad4 OTH exome

AF:

0.563

GnomAD4 genome

AF:

0.567

AC:

86226

AN:

152144

Hom.:

24932

Cov.:

AF XY:

0.563

AC XY:

41894

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.585

Gnomad4 AMR

AF:

0.577

Gnomad4 ASJ

AF:

0.576

Gnomad4 EAS

AF:

0.173

Gnomad4 SAS

AF:

0.657

Gnomad4 FIN

AF:

0.557

Gnomad4 NFE

AF:

0.575

Gnomad4 OTH

AF:

0.586

Alfa

AF:

0.573

Hom.:

66152

Bravo

AF:

0.568

TwinsUK

AF:

0.588

AC:

2180

ALSPAC

AF:

0.575

AC:

2216

ESP6500AA

AF:

0.579

AC:

2549

ESP6500EA

AF:

0.585

AC:

5034

ExAC

AF:

0.564

AC:

68484

Asia WGS

AF:

0.479

AC:

1665

AN:

3478

EpiCase

AF:

0.589

EpiControl

AF:

0.585

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.50

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.048

T;T

Eigen

Benign

-0.22

Eigen_PC

Benign

-0.17

FATHMM_MKL

Benign

0.24

LIST_S2

Benign

0.71

.;T

MetaRNN

Benign

0.0000035

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Uncertain

2.3

M;M

MutationTaster

Benign

0.77

P;P;P

PrimateAI

Uncertain

0.51

PROVEAN

Uncertain

-2.4

N;N

REVEL

Benign

0.034

Sift

Benign

0.036

D;D

Sift4G

Uncertain

0.0050

D;D

Polyphen

0.0020

B;B

Vest4

0.081

MPC

0.10

ClinPred

0.020

GERP RS

3.9

Varity_R

0.21

gMVP

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over