chr2-113130888-A-G

Position:

• chr2-113130888-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_173842.3(IL1RN):​c.206-157A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,046 control chromosomes in the GnomAD database, including 4,216 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.22 (4216 hom., cov: 30)
• Consequence: IL1RN NM_173842.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.03

Genes affected

IL1RN (HGNC:6000): (interleukin 1 receptor antagonist) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This protein inhibits the activities of interleukin 1, alpha (IL1A) and interleukin 1, beta (IL1B), and modulates a variety of interleukin 1 related immune and inflammatory responses, particularly in the acute phase of infection and inflammation. This gene and five other closely related cytokine genes form a gene cluster spanning approximately 400 kb on chromosome 2. A polymorphism of this gene is reported to be associated with increased risk of osteoporotic fractures and gastric cancer. Several alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 2-113130888-A-G is Benign according to our data. Variant chr2-113130888-A-G is described in ClinVar as [Benign]. Clinvar id is 1294768.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RN	NM_173842.3	c.206-157A>G		intron_variant		ENST00000409930.4	NP_776214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RN	ENST00000409930.4	c.206-157A>G		intron_variant		1	NM_173842.3	ENSP00000387173	P4

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32695 AN: 151930 Hom.: 4207 Cov.: 30

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.215 AC: 32733 AN: 152046 Hom.: 4216 Cov.: 30 AF XY: 0.218 AC XY: 16179 AN XY: 74296

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0771

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.241

Alfa AF: 0.231 Hom.: 672

Bravo AF: 0.206

Asia WGS AF: 0.198 AC: 688 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.51

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: rs448341; hg19: chr2-113888465; COSMIC: COSV52080128; COSMIC: COSV52080128;