12-68250838-T-A

Position:

• chr12-68250838-T-A

Variant summary

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

The NM_020525.5(IL22):​c.462+675A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,996 control chromosomes in the GnomAD database, including 16,369 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 0.46 (16369 hom., cov: 31)
• Consequence: IL22 NM_020525.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

IL22 (HGNC:14900): (interleukin 22) This gene is a member of the IL10 family of cytokines that mediate cellular inflammatory responses. The encoded protein functions in antimicrobial defense at mucosal surfaces and in tissue repair. This protein also has pro-inflammatory properties and plays a role in in the pathogenesis of several intestinal diseases. The encoded protein is a crucial cytokine that regulates host immunity in infectious diseases, including COVID-19 (disease caused by SARS-CoV-2). [provided by RefSeq, Dec 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL22	NM_020525.5	c.462+675A>T		intron_variant		ENST00000538666.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL22	ENST00000538666.6	c.462+675A>T		intron_variant		1	NM_020525.5	P1
IL22	ENST00000328087.6	c.462+675A>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69894 AN: 151880 Hom.: 16344 Cov.: 31

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.460 AC: 69964 AN: 151996 Hom.: 16369 Cov.: 31 AF XY: 0.464 AC XY: 34488 AN XY: 74298

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.505

Alfa AF: 0.278 Hom.: 682

Bravo AF: 0.464

Asia WGS AF: 0.592 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.044
DANN	Benign	0.41

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: rs1012356; hg19: chr12-68644618;