Genetic Variant IL17C:c.335+87T>C (chr16-88639396-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013278.4(IL17C):c.335+87T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 1,329,458 control chromosomes in the GnomAD database, including 347,090 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 0.74 ( 41537 hom., cov: 34)

Exomes 𝑓: 0.72 ( 305553 hom. )

Consequence

IL17C
NM_013278.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.386

Publications

10 publications found

Variant links:

Genes affected

IL17C (HGNC:5983): (interleukin 17C) The protein encoded by this gene is a T cell-derived cytokine that shares the sequence similarity with IL17. This cytokine was reported to stimulate the release of tumor necrosis factor alpha and interleukin 1 beta from a monocytic cell line. The expression of this cytokine was found to be restricted to activated T cells. [provided by RefSeq, Jul 2008]

IL17C 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013278.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17C	NM_013278.4	MANE Select	c.335+87T>C		intron	N/A	NP_037410.1	Q9P0M4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17C	ENST00000244241.5	TSL:1 MANE Select	c.335+87T>C		intron	N/A	ENSP00000244241.4	Q9P0M4
	IL17C	ENST00000569133.1	TSL:1	n.719+87T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.738

AC:

112118

AN:

152002

Hom.:

41498

Cov.:

show subpopulations

Gnomad AFR

AF:

0.797

Gnomad AMI

AF:

0.639

Gnomad AMR

AF:

0.719

Gnomad ASJ

AF:

0.798

Gnomad EAS

AF:

0.811

Gnomad SAS

AF:

0.798

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.710

Gnomad OTH

AF:

0.746

GnomAD4 exome

AF:

0.719

AC:

846086

AN:

1177338

Hom.:

305553

AF XY:

0.720

AC XY:

414155

AN XY:

575056

show subpopulations

African (AFR)

AF:

0.799

AC:

21132

AN:

26464

American (AMR)

AF:

0.690

AC:

15437

AN:

22358

Ashkenazi Jewish (ASJ)

AF:

0.799

AC:

14709

AN:

18410

East Asian (EAS)

AF:

0.839

AC:

28560

AN:

34056

South Asian (SAS)

AF:

0.787

AC:

49238

AN:

62550

European-Finnish (FIN)

AF:

0.623

AC:

19184

AN:

30788

Middle Eastern (MID)

AF:

0.799

AC:

2759

AN:

3452

European-Non Finnish (NFE)

AF:

0.709

AC:

658617

AN:

929424

Other (OTH)

AF:

0.731

AC:

36450

AN:

49836

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

11856

23711

35567

47422

59278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16916

33832

50748

67664

84580

<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:

0.738

AC:

112201

AN:

152120

Hom.:

41537

Cov.:

AF XY:

0.738

AC XY:

54840

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.797

AC:

33077

AN:

41514

American (AMR)

AF:

0.719

AC:

11007

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.798

AC:

2767

AN:

3468

East Asian (EAS)

AF:

0.810

AC:

4166

AN:

5144

South Asian (SAS)

AF:

0.799

AC:

3853

AN:

4822

European-Finnish (FIN)

AF:

0.632

AC:

6698

AN:

10590

Middle Eastern (MID)

AF:

0.816

AC:

240

AN:

294

European-Non Finnish (NFE)

AF:

0.710

AC:

48240

AN:

67952

Other (OTH)

AF:

0.742

AC:

1570

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1580

3161

4741

6322

7902

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.711

Hom.:

20513

Bravo

AF:

0.745

Asia WGS

AF:

0.786

AC:

2736

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

(source)

DANN

Benign

0.32

PhyloP100

-0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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