16-88639396-T-C

Position:

• chr16-88639396-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17C	NM_013278.4	c.335+87T>C		intron_variant		ENST00000244241.5	NP_037410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17C	ENST00000244241.5	c.335+87T>C		intron_variant		1	NM_013278.4	ENSP00000244241.4
IL17C	ENST00000569133.1	n.719+87T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112118 AN: 152002 Hom.: 41498 Cov.: 34

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

Gnomad4 AFR exome AF: 0.799

Gnomad4 AMR exome AF: 0.690

Gnomad4 ASJ exome AF: 0.799

Gnomad4 EAS exome AF: 0.839

Gnomad4 SAS exome AF: 0.787

Gnomad4 FIN exome AF: 0.623

Gnomad4 NFE exome AF: 0.709

Gnomad4 OTH exome AF: 0.731

GnomAD4 genome AF: 0.738 AC: 112201 AN: 152120 Hom.: 41537 Cov.: 34 AF XY: 0.738 AC XY: 54840 AN XY: 74334

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.742

Alfa AF: 0.721 Hom.: 13507

Bravo AF: 0.745

Asia WGS AF: 0.786 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.32

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

Other links and lift over

dbSNP: rs2254073; hg19: chr16-88705804; COSMIC: COSV54919234; COSMIC: COSV54919234;