Genetic Variant IL17REL:c.103-291C>T (chr22-50008955-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371417.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL17REL	NM_001371417.1	MANE Select	c.103-291C>T	intron	N/A	NP_001358346.1
IL17REL	NM_001371416.1		c.103-291C>T	intron	N/A	NP_001358345.1
IL17REL	NM_001001694.3		c.-70+28C>T	intron	N/A	NP_001001694.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL17REL	ENST00000695950.1	MANE Select	c.103-291C>T	intron	N/A	ENSP00000512282.1
IL17REL	ENST00000695951.1		c.103-291C>T	intron	N/A	ENSP00000512283.1
IL17REL	ENST00000389983.7	TSL:2	n.*66+28C>T	intron	N/A	ENSP00000374633.3

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

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.278

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.288

AC:

43821

AN:

152180

Hom.:

6431

Cov.:

AF XY:

0.288

AC XY:

21395

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.281

AC:

11659

AN:

41524

American (AMR)

AF:

0.311

AC:

4760

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.395

AC:

1369

AN:

3470

East Asian (EAS)

AF:

0.325

AC:

1681

AN:

5170

South Asian (SAS)

AF:

0.324

AC:

1562

AN:

4816

European-Finnish (FIN)

AF:

0.245

AC:

2593

AN:

10588

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.283

AC:

19228

AN:

67996

Other (OTH)

AF:

0.315

AC:

665

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1633

3266

4898

6531

8164

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.7

(source)

DANN

Benign

0.75

PhyloP100

0.20

PromoterAI

0.00010

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over