rs2254073

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-88639396-T-A
• chr16-88639396-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_013278.4(IL17C):​c.335+87T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0000017 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000170 AC: 2 AN: 1179010 Hom.: 0 AF XY: 0.00000174 AC XY: 1 AN XY: 575860

African (AFR) AF: 0.00 AC: 0 AN: 26486

American (AMR) AF: 0.00 AC: 0 AN: 22386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18428

East Asian (EAS) AF: 0.00 AC: 0 AN: 34066

South Asian (SAS) AF: 0.00 AC: 0 AN: 62606

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30798

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3454

European-Non Finnish (NFE) AF: 0.00000107 AC: 1 AN: 930880

Other (OTH) AF: 0.0000200 AC: 1 AN: 49906

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		-0.39

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;