rs7278931

Variant names:

• chr21-33300142-G-A
• rs7278931
• NM_001405850.1:c.805-8043G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-33300142-G-A
• chr21-33300142-G-T

Variant summary

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

The NM_001405850.1(IL10RB):​c.805-8043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,052 control chromosomes in the GnomAD database, including 4,000 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 0.22 (4000 hom., cov: 32)
• Consequence: IL10RB NM_001405850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 2 publications found

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]

IL10RB Gene-Disease associations (from GenCC):

• inflammatory bowel disease 25

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• IL10-related early-onset inflammatory bowel disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000294417 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL10RB	NM_001405850.1	c.805-8043G>A		intron_variant	Intron 6 of 6		NP_001392779.1
IL10RB	NM_001405849.1	c.805-8834G>A		intron_variant	Intron 6 of 6		NP_001392778.1
IL10RB	NR_175973.1	n.746-8834G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL10RB	ENST00000609556.3	c.805-8043G>A		intron_variant	Intron 6 of 6	5		ENSP00000489965.2
IL10RB	ENST00000637650.2	c.805-8834G>A		intron_variant	Intron 6 of 6	5		ENSP00000489716.2
ENSG00000294417	ENST00000723465.1	n.301-1195C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34085 AN: 151934 Hom.: 3996 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.224 AC: 34107 AN: 152052 Hom.: 4000 Cov.: 32 AF XY: 0.226 AC XY: 16788 AN XY: 74324

African (AFR) AF: 0.273 AC: 11325 AN: 41470

American (AMR) AF: 0.187 AC: 2855 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3470

East Asian (EAS) AF: 0.387 AC: 2001 AN: 5172

South Asian (SAS) AF: 0.244 AC: 1173 AN: 4814

European-Finnish (FIN) AF: 0.253 AC: 2672 AN: 10558

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12990 AN: 67966

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.214 Hom.: 432

Bravo AF: 0.223

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7278931; hg19: chr21-34672447;