Variant rs137866 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001371417.1(IL17REL):c.103-291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,212 control chromosomes in the GnomAD database, including 6,432 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 0.29 ( 6431 hom., cov: 32)

Exomes 𝑓: 0.31 ( 1 hom. )

Consequence

IL17REL
NM_001371417.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.203

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
IL17REL	NM_001371417.1 linkuse as main transcript	c.103-291C>T	intron_variant	ENST00000695950.1	NP_001358346.1
IL17REL	NM_001001694.3 linkuse as main transcript	c.-70+28C>T	intron_variant		NP_001001694.2
IL17REL	NM_001371416.1 linkuse as main transcript	c.103-291C>T	intron_variant		NP_001358345.1
IL17REL	XR_001755245.2 linkuse as main transcript	n.222-291C>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
IL17REL	ENST00000695950.1 linkuse as main transcript	c.103-291C>T	intron_variant		NM_001371417.1	ENSP00000512282	A2
IL17REL	ENST00000695951.1 linkuse as main transcript	c.103-291C>T	intron_variant			ENSP00000512283	P2
IL17REL	ENST00000389983.7 linkuse as main transcript	c.*66+28C>T	intron_variant, NMD_transcript_variant	2		ENSP00000374633

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43777

AN:

152062

Hom.:

6418

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.325

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.312

GnomAD4 exome

AF:

0.313

AC:

AN:

Hom.:

Cov.:

AF XY:

0.364

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.400

Gnomad4 NFE exome

AF:

0.278

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.288

AC:

43821

AN:

152180

Hom.:

6431

Cov.:

AF XY:

0.288

AC XY:

21395

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.311

Gnomad4 ASJ

AF:

0.395

Gnomad4 EAS

AF:

0.325

Gnomad4 SAS

AF:

0.324

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.315

Alfa

AF:

0.297

Hom.:

1257

Bravo

AF:

0.292

Asia WGS

AF:

0.289

AC:

1008

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

2.7

DANN

Benign

0.75

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over