rs3024494

Variant names:

• chr1-206770006-T-A
• rs3024494
• NM_000572.3:c.379-112A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-206770006-T-A
• chr1-206770006-T-C
• chr1-206770006-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000572.3(IL10):​c.379-112A>T variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL10 NM_000572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

IL10 (HGNC:5962): (interleukin 10) The protein encoded by this gene is a cytokine produced primarily by monocytes and to a lesser extent by lymphocytes. This cytokine has pleiotropic effects in immunoregulation and inflammation. It down-regulates the expression of Th1 cytokines, MHC class II Ags, and costimulatory molecules on macrophages. It also enhances B cell survival, proliferation, and antibody production. This cytokine can block NF-kappa B activity, and is involved in the regulation of the JAK-STAT signaling pathway. Knockout studies in mice suggested the function of this cytokine as an essential immunoregulator in the intestinal tract. Mutations in this gene are associated with an increased susceptibility to HIV-1 infection and rheumatoid arthritis. [provided by RefSeq, May 2020]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL10	NM_000572.3	c.379-112A>T		intron_variant	Intron 3 of 4	ENST00000423557.1	NP_000563.1
IL10	NM_001382624.1	c.124-112A>T		intron_variant	Intron 1 of 2		NP_001369553.1
IL10	NR_168466.1	n.675+76A>T		intron_variant	Intron 4 of 5
IL10	NR_168467.1	n.206-112A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL10	ENST00000423557.1	c.379-112A>T		intron_variant	Intron 3 of 4	1	NM_000572.3	ENSP00000412237.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 640694 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 343998

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 17558

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 36832

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 20640

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 33854

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 65948

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 48056

Gnomad4 NFE exome AF: 0.00 AC: 0 AN: 381320

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 33238

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 20948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.50

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: rs3024494; hg19: chr1-206943351;