dbSNP rs137866: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IL17REL	NM_001371417.1 link	c.103-291C>T	intron_variant	Intron 1 of 14	ENST00000695950.1	NP_001358346.1
IL17REL	NM_001371416.1 link	c.103-291C>T	intron_variant	Intron 1 of 14		NP_001358345.1
IL17REL	NM_001001694.3 link	c.-70+28C>T	intron_variant	Intron 2 of 14		NP_001001694.2	Q6ZVW7
IL17REL	XR_001755245.2 link	n.222-291C>T	intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL17REL	ENST00000695950.1 link	c.103-291C>T	intron_variant	Intron 1 of 14		NM_001371417.1	ENSP00000512282.1	A0A8Q3WKV1
IL17REL	ENST00000695951.1 link	c.103-291C>T	intron_variant	Intron 1 of 14			ENSP00000512283.1	A0A8Q3WLX3
IL17REL	ENST00000389983.7 link	n.*66+28C>T	intron_variant	Intron 2 of 14	2		ENSP00000374633.3	Q6ZVW7

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over