NM_173161.3:c.72T>C

Variant names:

• chr2-113074368-T-C
• rs3811058
• NM_173161.3:c.72T>C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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

Verdict is Benign. Variant got -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	c.72T>C	p.Asp24Asp	synonymous_variant	Exon 3 of 5	ENST00000341010.6	NP_775184.1
IL1F10	NM_032556.6	c.72T>C	p.Asp24Asp	synonymous_variant	Exon 2 of 4		NP_115945.4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14209 AN: 152154 Hom.: 1267 Cov.: 32

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

GnomAD3 exomes AF: 0.129 AC: 32401 AN: 251306 Hom.: 4085 AF XY: 0.125 AC XY: 16957 AN XY: 135822

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 SAS exome AF: 0.105

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.: 30 AF XY: 0.0925 AC XY: 67234 AN XY: 726814

Gnomad4 AFR exome AF: 0.0515

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.140

Gnomad4 EAS exome AF: 0.567

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0901

Gnomad4 NFE exome AF: 0.0708

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0933 AC: 14210 AN: 152272 Hom.: 1260 Cov.: 32 AF XY: 0.0990 AC XY: 7371 AN XY: 74470

Gnomad4 AFR AF: 0.0556

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0934

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.107

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
DANN	Benign	0.26

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

LitVar

Other links and lift over

dbSNP: rs3811058; hg19: chr2-113831945; COSMIC: COSV61750580; COSMIC: COSV61750580;