NM_173161.3:c.131T>C

Variant names:

• chr2-113074735-T-C
• rs6761276
• NM_173161.3:c.131T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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.

• Frequency:
  • Genomes: 𝑓 0.57 (24932 hom., cov: 33)
  • Exomes 𝑓: 0.57 (243047 hom.)
• Consequence: IL1F10 NM_173161.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 56 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173161.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1F10	NM_173161.3	MANE Select	c.131T>C	p.Ile44Thr	missense	Exon 4 of 5	NP_775184.1
	IL1F10	NM_032556.6		c.131T>C	p.Ile44Thr	missense	Exon 3 of 4	NP_115945.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1F10	ENST00000341010.6	TSL:1 MANE Select	c.131T>C	p.Ile44Thr	missense	Exon 4 of 5	ENSP00000341794.2
	IL1F10	ENST00000393197.3	TSL:1	c.131T>C	p.Ile44Thr	missense	Exon 3 of 4	ENSP00000376893.2
	IL1F10	ENST00000496265.1	TSL:1	n.197T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86156 AN: 152026 Hom.: 24901 Cov.: 33

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

GnomAD2 exomes AF: 0.560 AC: 140726 AN: 251370 AF XY: 0.569

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 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.: 44 AF XY: 0.575 AC XY: 417007 AN XY: 725772

African (AFR) AF: 0.584 AC: 19493 AN: 33398

American (AMR) AF: 0.564 AC: 25217 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 14726 AN: 26116

East Asian (EAS) AF: 0.148 AC: 5879 AN: 39698

South Asian (SAS) AF: 0.684 AC: 58964 AN: 86212

European-Finnish (FIN) AF: 0.548 AC: 29258 AN: 53388

Middle Eastern (MID) AF: 0.684 AC: 3936 AN: 5758

European-Non Finnish (NFE) AF: 0.579 AC: 641925 AN: 1109036

Other (OTH) AF: 0.563 AC: 33956 AN: 60276

GnomAD4 genome AF: 0.567 AC: 86226 AN: 152144 Hom.: 24932 Cov.: 33 AF XY: 0.563 AC XY: 41894 AN XY: 74374

African (AFR) AF: 0.585 AC: 24269 AN: 41492

American (AMR) AF: 0.577 AC: 8824 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1998 AN: 3470

East Asian (EAS) AF: 0.173 AC: 893 AN: 5176

South Asian (SAS) AF: 0.657 AC: 3172 AN: 4828

European-Finnish (FIN) AF: 0.557 AC: 5901 AN: 10596

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39085 AN: 67968

Other (OTH) AF: 0.586 AC: 1238 AN: 2114

Alfa AF: 0.572 Hom.: 97716

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Benign	-0.71	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.048	T
Eigen	Benign	-0.22
Eigen_PC	Benign	-0.17
FATHMM_MKL	Benign	0.24	N
LIST_S2	Benign	0.71	T
MetaRNN	Benign	0.0000035	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		1.0
PrimateAI	Uncertain	0.51	T
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.034
Sift	Benign	0.036	D
Sift4G	Uncertain	0.0050	D
Polyphen		0.0020	B
Vest4		0.081
MPC		0.10
ClinPred		0.020	T
GERP RS		3.9
Varity_R		0.21
gMVP		0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6761276; hg19: chr2-113832312; COSMIC: COSV61750606;