rs28366

Variant names:

• chr6-137144950-C-A
• rs28366
• NM_052962.3:c.*674G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-137144950-C-A
• chr6-137144950-C-G
• chr6-137144950-C-T

Variant summary

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

The NM_052962.3(IL22RA2):​c.*674G>T variant causes a 3 prime UTR 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: 32)
• Consequence: IL22RA2 NM_052962.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 7 publications found

Genes affected

IL22RA2 (HGNC:14901): (interleukin 22 receptor subunit alpha 2) This gene encodes a member of the class II cytokine receptor family. The encoded soluble protein specifically binds to and inhibits interleukin 22 activity by blocking the interaction of interleukin 22 with its cell surface receptor. The encoded protein may be important in the regulation of inflammatory response, and has been implicated in the regulation of tumorigenesis in the colon. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2013]

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=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052962.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL22RA2	NM_052962.3	MANE Select	c.*674G>T		3_prime_UTR	Exon 7 of 7	NP_443194.1
	IL22RA2	NM_181309.2		c.*674G>T		3_prime_UTR	Exon 6 of 6	NP_851826.1
	IL22RA2	NM_181310.2		c.*807G>T		3_prime_UTR	Exon 5 of 5	NP_851827.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL22RA2	ENST00000296980.7	TSL:1 MANE Select	c.*674G>T		3_prime_UTR	Exon 7 of 7	ENSP00000296980.2
	IL22RA2	ENST00000349184.9	TSL:1	c.*674G>T		3_prime_UTR	Exon 6 of 6	ENSP00000296979.4
	IL22RA2	ENST00000339602.3	TSL:1	c.*807G>T		3_prime_UTR	Exon 5 of 5	ENSP00000340920.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 60407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.40
PhyloP100		-0.38

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

Other links and lift over

dbSNP: rs28366; hg19: chr6-137466087;