rs1610997

Positions:

• chr21-33287341-G-GGTTT
• chr21-33287341-GGTTT-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000628.5(IL10RB):​c.647-754_647-751dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20561 hom., cov: 0)
• Consequence: IL10RB NM_000628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

IL10RB (HGNC:5965): (interleukin 10 receptor subunit beta) The protein encoded by this gene belongs to the cytokine receptor family. It is an accessory chain essential for the active interleukin 10 receptor complex. Coexpression of this and IL10RA proteins has been shown to be required for IL10-induced signal transduction. This gene and three other interferon receptor genes, IFAR2, IFNAR1, and IFNGR2, form a class II cytokine receptor gene cluster located in a small region on chromosome 21. [provided by RefSeq, Jul 2008]

IFNAR2-IL10RB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL10RB	NM_000628.5	c.647-754_647-751dup		intron_variant		ENST00000290200.7	NP_000619.3
IFNAR2-IL10RB	NM_001414505.1	c.1307-754_1307-751dup		intron_variant			NP_001401434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL10RB	ENST00000290200.7	c.647-754_647-751dup		intron_variant		1	NM_000628.5	ENSP00000290200	P2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76458 AN: 150756 Hom.: 20525 Cov.: 0

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.507 AC: 76533 AN: 150872 Hom.: 20561 Cov.: 0 AF XY: 0.502 AC XY: 37028 AN XY: 73710

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.482

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1610997; hg19: chr21-34659646;