rs771331743

Variant names:

• chr2-113074758-C-A
• rs771331743
• NM_173161.3:c.154C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-113074758-C-A
• chr2-113074758-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_173161.3(IL1F10):​c.154C>A​(p.Arg52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R52H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: IL1F10 NM_173161.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• Publications: 0 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: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.39356384).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1F10	NM_173161.3	c.154C>A	p.Arg52Ser	missense_variant	Exon 4 of 5	ENST00000341010.6	NP_775184.1
IL1F10	NM_032556.6	c.154C>A	p.Arg52Ser	missense_variant	Exon 3 of 4		NP_115945.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1F10	ENST00000341010.6	c.154C>A	p.Arg52Ser	missense_variant	Exon 4 of 5	1	NM_173161.3	ENSP00000341794.2
IL1F10	ENST00000393197.3	c.154C>A	p.Arg52Ser	missense_variant	Exon 3 of 4	1		ENSP00000376893.2
IL1F10	ENST00000496265.1	n.220C>A		non_coding_transcript_exon_variant	Exon 1 of 2	1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0018	T;T
Eigen	Benign	0.16
Eigen_PC	Benign	0.20
FATHMM_MKL	Benign	0.62	D
LIST_S2	Benign	0.73	.;T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.39	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	L;L
PhyloP100		2.4
PrimateAI	Benign	0.42	T
PROVEAN	Benign	0.48	N;N
REVEL	Benign	0.15
Sift	Benign	0.77	T;T
Sift4G	Benign	0.81	T;T
Polyphen		0.92	P;P
Vest4		0.49
MutPred		0.48		Loss of solvent accessibility (P = 0.0238);Loss of solvent accessibility (P = 0.0238);
MVP		0.36
MPC		0.21
ClinPred		0.89	D
GERP RS		5.1
Varity_R		0.86
gMVP		0.38
Mutation Taster		=93/7	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs771331743; hg19: chr2-113832335; COSMIC: COSV61750678;