16-57415094-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002987.3(CCL17):āc.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
NM_002987.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.33
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 |
---|---|---|---|---|---|---|---|
CCL17 | NM_002987.3 | c.84T>C | p.Asn28= | synonymous_variant | 3/4 | ENST00000219244.9 | |
CCL17 | XM_017023530.2 | c.171T>C | p.Asn57= | synonymous_variant | 5/6 | ||
CCL17 | XM_011523256.3 | c.168T>C | p.Asn56= | synonymous_variant | 5/6 | ||
CCL17 | XM_047434448.1 | c.84T>C | p.Asn28= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL17 | ENST00000219244.9 | c.84T>C | p.Asn28= | synonymous_variant | 3/4 | 1 | NM_002987.3 | P1 | |
CCL17 | ENST00000616880.1 | c.84T>C | p.Asn28= | synonymous_variant | 2/3 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0141 AC: 2147AN: 152078Hom.: 53 Cov.: 32
GnomAD3 genomes
AF:
AC:
2147
AN:
152078
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00389 AC: 977AN: 251384Hom.: 25 AF XY: 0.00294 AC XY: 400AN XY: 135866
GnomAD3 exomes
AF:
AC:
977
AN:
251384
Hom.:
AF XY:
AC XY:
400
AN XY:
135866
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00175 AC: 2556AN: 1460908Hom.: 53 Cov.: 30 AF XY: 0.00158 AC XY: 1148AN XY: 726864
GnomAD4 exome
AF:
AC:
2556
AN:
1460908
Hom.:
Cov.:
30
AF XY:
AC XY:
1148
AN XY:
726864
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0141 AC: 2147AN: 152196Hom.: 54 Cov.: 32 AF XY: 0.0134 AC XY: 996AN XY: 74420
GnomAD4 genome
AF:
AC:
2147
AN:
152196
Hom.:
Cov.:
32
AF XY:
AC XY:
996
AN XY:
74420
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
9
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 23, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at