16-57415094-T-C

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002987.3(CCL17):ā€‹c.84T>Cā€‹(p.Asn28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00292 in 1,613,104 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.014 ( 54 hom., cov: 32)
Exomes š‘“: 0.0017 ( 53 hom. )

Consequence

CCL17
NM_002987.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.33
Variant links:
Genes affected
CCL17 (HGNC:10615): (C-C motif chemokine ligand 17) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 16. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for T lymphocytes, but not monocytes or granulocytes. The product of this gene binds to chemokine receptors CCR4 and CCR8. This chemokine plays important roles in T cell development in thymus as well as in trafficking and activation of mature T cells. [provided by RefSeq, Sep 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 16-57415094-T-C is Benign according to our data. Variant chr16-57415094-T-C is described in ClinVar as [Benign]. Clinvar id is 717786.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.33 with no splicing effect.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0535 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCL17NM_002987.3 linkuse as main transcriptc.84T>C p.Asn28= synonymous_variant 3/4 ENST00000219244.9
CCL17XM_017023530.2 linkuse as main transcriptc.171T>C p.Asn57= synonymous_variant 5/6
CCL17XM_011523256.3 linkuse as main transcriptc.168T>C p.Asn56= synonymous_variant 5/6
CCL17XM_047434448.1 linkuse as main transcriptc.84T>C p.Asn28= synonymous_variant 2/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCL17ENST00000219244.9 linkuse as main transcriptc.84T>C p.Asn28= synonymous_variant 3/41 NM_002987.3 P1
CCL17ENST00000616880.1 linkuse as main transcriptc.84T>C p.Asn28= synonymous_variant 2/31 P1

Frequencies

GnomAD3 genomes
AF:
0.0141
AC:
2147
AN:
152078
Hom.:
53
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0482
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00511
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000529
Gnomad OTH
AF:
0.0158
GnomAD3 exomes
AF:
0.00389
AC:
977
AN:
251384
Hom.:
25
AF XY:
0.00294
AC XY:
400
AN XY:
135866
show subpopulations
Gnomad AFR exome
AF:
0.0504
Gnomad AMR exome
AF:
0.00220
Gnomad ASJ exome
AF:
0.0000993
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000554
Gnomad OTH exome
AF:
0.00244
GnomAD4 exome
AF:
0.00175
AC:
2556
AN:
1460908
Hom.:
53
Cov.:
30
AF XY:
0.00158
AC XY:
1148
AN XY:
726864
show subpopulations
Gnomad4 AFR exome
AF:
0.0556
Gnomad4 AMR exome
AF:
0.00237
Gnomad4 ASJ exome
AF:
0.000191
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000162
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000297
Gnomad4 OTH exome
AF:
0.00360
GnomAD4 genome
AF:
0.0141
AC:
2147
AN:
152196
Hom.:
54
Cov.:
32
AF XY:
0.0134
AC XY:
996
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0481
Gnomad4 AMR
AF:
0.00510
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000529
Gnomad4 OTH
AF:
0.0156
Alfa
AF:
0.00672
Hom.:
13
Bravo
AF:
0.0166
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.000491
EpiControl
AF:
0.000652

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpApr 23, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.83
DANN
Benign
0.42

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: rs61737346; hg19: chr16-57449006; API