22-49999334-C-A

Position:

• chr22-49999334-C-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001371417.1(IL17REL):​c.774G>T​(p.Ala258Ala) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: IL17REL NM_001371417.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.01

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]

IL17REL (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 22-49999334-C-A is Benign according to our data. Variant chr22-49999334-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3389803.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-4.01 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17REL	NM_001371417.1	c.774G>T	p.Ala258Ala	synonymous_variant	9/15	ENST00000695950.1	NP_001358346.1
IL17REL	NM_001371416.1	c.774G>T	p.Ala258Ala	synonymous_variant	9/15		NP_001358345.1
IL17REL	NM_001001694.3	c.558G>T	p.Ala186Ala	synonymous_variant	9/15		NP_001001694.2
IL17REL	XR_001755245.2	n.893G>T		non_coding_transcript_exon_variant	9/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17REL	ENST00000695950.1	c.774G>T	p.Ala258Ala	synonymous_variant	9/15		NM_001371417.1	ENSP00000512282.1
IL17REL	ENST00000695951.1	c.774G>T	p.Ala258Ala	synonymous_variant	9/15			ENSP00000512283.1
IL17REL	ENST00000389983.7	n.*693G>T		non_coding_transcript_exon_variant	9/15	2		ENSP00000374633.3
IL17REL	ENST00000389983.7	n.*693G>T		3_prime_UTR_variant	9/15	2		ENSP00000374633.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2024

IL17REL: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.2
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-50437763;