6-52236808-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_052872.4(IL17F):​c.*123C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00974 in 798,730 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0084 ( 9 hom., cov: 32)
Exomes 𝑓: 0.010 ( 46 hom. )

Consequence

IL17F
NM_052872.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.454
Variant links:
Genes affected
IL17F (HGNC:16404): (interleukin 17F) The protein encoded by this gene is a cytokine that shares sequence similarity with IL17. This cytokine is expressed by activated T cells, and has been shown to stimulate the production of several other cytokines, including IL6, IL8, and CSF2/GM_CSF. This cytokine is also found to inhibit the angiogenesis of endothelial cells and induce endothelial cells to produce IL2, TGFB1/TGFB, and monocyte chemoattractant protein-1. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 6-52236808-G-A is Benign according to our data. Variant chr6-52236808-G-A is described in ClinVar as [Benign]. Clinvar id is 357465.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 1280 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL17FNM_052872.4 linkuse as main transcriptc.*123C>T 3_prime_UTR_variant 3/3 ENST00000336123.5 NP_443104.1
IL17FXM_011514276.1 linkuse as main transcriptc.*123C>T 3_prime_UTR_variant 4/4 XP_011512578.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL17FENST00000336123.5 linkuse as main transcriptc.*123C>T 3_prime_UTR_variant 3/31 NM_052872.4 ENSP00000337432 P1
IL17FENST00000478427.1 linkuse as main transcriptn.799C>T non_coding_transcript_exon_variant 2/21
IL17FENST00000699946.1 linkuse as main transcriptc.*123C>T 3_prime_UTR_variant 4/4 ENSP00000514702 P1

Frequencies

GnomAD3 genomes
AF:
0.00841
AC:
1279
AN:
152118
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00229
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.00471
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00332
Gnomad FIN
AF:
0.0194
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0126
Gnomad OTH
AF:
0.00621
GnomAD4 exome
AF:
0.0100
AC:
6497
AN:
646494
Hom.:
46
Cov.:
7
AF XY:
0.00975
AC XY:
3418
AN XY:
350570
show subpopulations
Gnomad4 AFR exome
AF:
0.00189
Gnomad4 AMR exome
AF:
0.00371
Gnomad4 ASJ exome
AF:
0.00223
Gnomad4 EAS exome
AF:
0.0000278
Gnomad4 SAS exome
AF:
0.00299
Gnomad4 FIN exome
AF:
0.0238
Gnomad4 NFE exome
AF:
0.0123
Gnomad4 OTH exome
AF:
0.00796
GnomAD4 genome
AF:
0.00841
AC:
1280
AN:
152236
Hom.:
9
Cov.:
32
AF XY:
0.00824
AC XY:
613
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.00229
Gnomad4 AMR
AF:
0.00471
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00332
Gnomad4 FIN
AF:
0.0194
Gnomad4 NFE
AF:
0.0126
Gnomad4 OTH
AF:
0.00662
Alfa
AF:
0.00921
Hom.:
0
Bravo
AF:
0.00712
Asia WGS
AF:
0.00664
AC:
23
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Candidiasis, familial, 6 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.55
DANN
Benign
0.58

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs189630805; hg19: chr6-52101606; COSMIC: COSV60233639; API