rs12469822

Variant names:

• chr2-113072986-G-A
• rs12469822
• NM_173161.3:c.32+216G>A

Variant summary

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

The NM_173161.3(IL1F10):​c.32+216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,110 control chromosomes in the GnomAD database, including 19,333 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 0.47 (19333 hom., cov: 32)
• Consequence: IL1F10 NM_173161.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 8 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 (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1F10	NM_173161.3	c.32+216G>A		intron_variant	Intron 2 of 4	ENST00000341010.6	NP_775184.1
IL1F10	NM_032556.6	c.32+216G>A		intron_variant	Intron 1 of 3		NP_115945.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1F10	ENST00000341010.6	c.32+216G>A		intron_variant	Intron 2 of 4	1	NM_173161.3	ENSP00000341794.2
IL1F10	ENST00000393197.3	c.32+216G>A		intron_variant	Intron 1 of 3	1		ENSP00000376893.2

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71795 AN: 151992 Hom.: 19319 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.510

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.472 AC: 71822 AN: 152110 Hom.: 19333 Cov.: 32 AF XY: 0.473 AC XY: 35196 AN XY: 74350

African (AFR) AF: 0.213 AC: 8851 AN: 41516

American (AMR) AF: 0.530 AC: 8106 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1988 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1084 AN: 5182

South Asian (SAS) AF: 0.672 AC: 3240 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6134 AN: 10562

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40510 AN: 67964

Other (OTH) AF: 0.511 AC: 1080 AN: 2112

Alfa AF: 0.560 Hom.: 23224

Bravo AF: 0.454

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs12469822; hg19: chr2-113830563;