rs5771222

chr22-50007275-T-C

Variant summary

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

The NM_001371417.1(IL17REL):c.130+1362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,932 control chromosomes in the GnomAD database, including 22,875 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 0.54 (22875 hom., cov: 33)
• Consequence: IL17REL NM_001371417.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

IL17REL (HGNC:33808): (interleukin 17 receptor E like) Predicted to enable interleukin-17 receptor activity. Predicted to be involved in cytokine-mediated signaling pathway. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17REL	NM_001371417.1	c.130+1362A>G		intron_variant		ENST00000695950.1
IL17REL	NM_001001694.3	c.-42+1362A>G		intron_variant
IL17REL	NM_001371416.1	c.130+1362A>G		intron_variant
IL17REL	XR_001755245.2	n.249+1362A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17REL	ENST00000695950.1	c.130+1362A>G		intron_variant			NM_001371417.1	A2
IL17REL	ENST00000695951.1	c.130+1362A>G		intron_variant				P2
IL17REL	ENST00000389983.7	c.*94+1362A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82394 AN: 151814 Hom.: 22852 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.543 AC: 82469 AN: 151932 Hom.: 22875 Cov.: 33 AF XY: 0.548 AC XY: 40717 AN XY: 74236

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.526

Alfa AF: 0.514 Hom.: 4253

Bravo AF: 0.532

Asia WGS AF: 0.636 AC: 2210 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.2
Dann	Benign	0.45

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: rs5771222; hg19: chr22-50445704;