16-88639396-T-C

Variant names:

• chr16-88639396-T-C
• rs2254073
• NM_013278.4:c.335+87T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17C	NM_013278.4	c.335+87T>C		intron_variant	Intron 2 of 2	ENST00000244241.5	NP_037410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17C	ENST00000244241.5	c.335+87T>C		intron_variant	Intron 2 of 2	1	NM_013278.4	ENSP00000244241.4
IL17C	ENST00000569133.1	n.719+87T>C		intron_variant	Intron 1 of 1	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

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

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

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.32
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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