rs8134731

Variant names:

• chr21-33299227-T-C
• rs8134731
• NM_001405850.1:c.805-8958T>C

Your query was ambiguous. Multiple possible variants found:

• chr21-33299227-T-C
• chr21-33299227-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001405850.1(IL10RB):​c.805-8958T>C 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 151,938 control chromosomes in the GnomAD database, including 3,932 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 (3932 hom., cov: 32)
• Consequence: IL10RB NM_001405850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL10RB	NM_001405850.1	c.805-8958T>C		intron_variant	Intron 6 of 6		NP_001392779.1
IL10RB	NM_001405849.1	c.805-9749T>C		intron_variant	Intron 6 of 6		NP_001392778.1
IL10RB	NR_175973.1	n.746-9749T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL10RB	ENST00000609556.3	c.805-8958T>C		intron_variant	Intron 6 of 6	5		ENSP00000489965.2
IL10RB	ENST00000637650.2	c.805-9749T>C		intron_variant	Intron 6 of 6	5		ENSP00000489716.2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33960 AN: 151820 Hom.: 3928 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.252

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: 33983 AN: 151938 Hom.: 3932 Cov.: 32 AF XY: 0.225 AC XY: 16721 AN XY: 74256

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.203

Alfa AF: 0.208 Hom.: 494

Bravo AF: 0.223

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8134731; hg19: chr21-34671532;