rs12469822

Positions:

• chr2-113072986-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
IL1F10	NM_173161.3	c.32+216G>A		intron_variant		ENST00000341010.6
IL1F10	NM_032556.6	c.32+216G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1F10	ENST00000341010.6	c.32+216G>A		intron_variant		1	NM_173161.3	P1
IL1F10	ENST00000393197.3	c.32+216G>A		intron_variant		1		P1

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.511

Alfa AF: 0.566 Hom.: 16872

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs12469822; hg19: chr2-113830563;