Variant rs5771069 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001371416.1(IL17REL):c.1214T>C(p.Leu405Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,558,162 control chromosomes in the GnomAD database, including 220,840 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.55 ( 23630 hom., cov: 34)

Exomes 𝑓: 0.52 ( 197210 hom. )

Consequence

IL17REL
NM_001371416.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.83

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.0144996E-6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17REL	NM_001371417.1 link	c.1281T>C	p.Ala427Ala	synonymous_variant	14/15	ENST00000695950.1	NP_001358346.1
IL17REL	NM_001371416.1 link	c.1214T>C	p.Leu405Pro	missense_variant	14/15		NP_001358345.1
IL17REL	NM_001001694.3 link	c.998T>C	p.Leu333Pro	missense_variant	14/15		NP_001001694.2	Q6ZVW7
IL17REL	XR_001755245.2 link	n.1400T>C		non_coding_transcript_exon_variant	14/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IL17REL	ENST00000695950.1 link	c.1281T>C	p.Ala427Ala	synonymous_variant	14/15		NM_001371417.1	ENSP00000512282.1	A0A8Q3WKV1
IL17REL	ENST00000695951.1 link	c.1214T>C	p.Leu405Pro	missense_variant	14/15			ENSP00000512283.1	A0A8Q3WLX3
IL17REL	ENST00000389983.7 link	n.*1133T>C		non_coding_transcript_exon_variant	14/15	2		ENSP00000374633.3	Q6ZVW7
IL17REL	ENST00000389983.7 link	n.*1133T>C		3_prime_UTR_variant	14/15	2		ENSP00000374633.3	Q6ZVW7

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83926

AN:

151954

Hom.:

23604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.616

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.765

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.564

AC:

104593

AN:

185426

Hom.:

30121

AF XY:

0.569

AC XY:

56978

AN XY:

100172

show subpopulations

Gnomad AFR exome

AF:

0.615

Gnomad AMR exome

AF:

0.544

Gnomad ASJ exome

AF:

0.579

Gnomad EAS exome

AF:

0.562

Gnomad SAS exome

AF:

0.768

Gnomad FIN exome

AF:

0.581

Gnomad NFE exome

AF:

0.507

Gnomad OTH exome

AF:

0.560

GnomAD4 exome

AF:

0.525

AC:

738064

AN:

1406090

Hom.:

197210

Cov.:

AF XY:

0.531

AC XY:

370033

AN XY:

696380

show subpopulations

Gnomad4 AFR exome

AF:

0.623

Gnomad4 AMR exome

AF:

0.530

Gnomad4 ASJ exome

AF:

0.583

Gnomad4 EAS exome

AF:

0.532

Gnomad4 SAS exome

AF:

0.764

Gnomad4 FIN exome

AF:

0.579

Gnomad4 NFE exome

AF:

0.499

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.552

AC:

84008

AN:

152072

Hom.:

23630

Cov.:

AF XY:

0.558

AC XY:

41492

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.616

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.567

Gnomad4 SAS

AF:

0.764

Gnomad4 FIN

AF:

0.588

Gnomad4 NFE

AF:

0.503

Gnomad4 OTH

AF:

0.536

Alfa

AF:

0.521

Hom.:

30068

Bravo

AF:

0.542

TwinsUK

AF:

0.505

AC:

1872

ALSPAC

AF:

0.503

AC:

1937

ESP6500AA

AF:

0.606

AC:

2651

ESP6500EA

AF:

0.502

AC:

4311

ExAC

AF:

0.548

AC:

65158

Asia WGS

AF:

0.645

AC:

2244

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.040

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.11

DANN

Benign

0.62

DEOGEN2

Benign

0.00062

T;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00047

LIST_S2

Benign

0.19

T;.

MetaRNN

Benign

0.0000010

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-0.20

N;N

PrimateAI

Benign

0.30

PROVEAN

Benign

1.0

N;N

REVEL

Benign

0.014

Sift

Benign

0.16

T;T

Sift4G

Benign

0.30

T;T

Polyphen

0.0

B;B

Vest4

0.027

MPC

0.35

ClinPred

0.0072

GERP RS

-4.3

Varity_R

0.030

gMVP

0.54

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

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