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GeneBe

16-57382414-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_002996.6(CX3CL1):c.576C>T(p.Ser192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,612,600 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 7 hom., cov: 32)
Exomes 𝑓: 0.00061 ( 9 hom. )

Consequence

CX3CL1
NM_002996.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.04
Variant links:
Genes affected
CX3CL1 (HGNC:10647): (C-X3-C motif chemokine ligand 1) This gene belongs to the CX3C subgroup of chemokines, characterized by the number of amino acids located between the conserved cysteine residues. This is the only member of the CX3C subgroup, which contains three amino acids between cysteine residues, resulting in a Cys-X-X-X-Cys configuration. The encoded protein contains an extended mucin-like stalk with a chemokine domain on top, and exists in both a membrane-anchored form where it acts as a binding molecule, or, in soluble form, as a chemotactic cytokine. The mature form of this protein can be cleaved at the cell surface, yielding different soluble forms that can interact with the G-protein coupled receptor, C-X3-C motif chemokine receptor 1 gene product. This gene plays a role in a wide range of diseases, including cancer, vasculitis, neuropathies, atherosclerosis, inflammatory diseases, and in human immunodeficiency virus infections. [provided by RefSeq, Sep 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 16-57382414-C-T is Benign according to our data. Variant chr16-57382414-C-T is described in ClinVar as [Benign]. Clinvar id is 711165.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.04 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00585 (891/152278) while in subpopulation AFR AF= 0.0202 (839/41554). AF 95% confidence interval is 0.0191. There are 7 homozygotes in gnomad4. There are 446 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
High Homozygotes in GnomAd at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CX3CL1NM_002996.6 linkuse as main transcriptc.576C>T p.Ser192= synonymous_variant 3/3 ENST00000006053.7
CX3CL1NM_001304392.3 linkuse as main transcriptc.321C>T p.Ser107= synonymous_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CX3CL1ENST00000006053.7 linkuse as main transcriptc.576C>T p.Ser192= synonymous_variant 3/31 NM_002996.6 P4
CX3CL1ENST00000565912.1 linkuse as main transcriptc.462C>T p.Ser154= synonymous_variant 2/21
CX3CL1ENST00000563383.1 linkuse as main transcriptc.594C>T p.Ser198= synonymous_variant 3/35 A2
CX3CL1ENST00000564948.1 linkuse as main transcriptc.*287C>T 3_prime_UTR_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.00584
AC:
889
AN:
152160
Hom.:
7
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0202
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00190
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.00384
GnomAD3 exomes
AF:
0.00141
AC:
351
AN:
248690
Hom.:
2
AF XY:
0.00106
AC XY:
143
AN XY:
134892
show subpopulations
Gnomad AFR exome
AF:
0.0183
Gnomad AMR exome
AF:
0.00119
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000981
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000623
Gnomad OTH exome
AF:
0.000987
GnomAD4 exome
AF:
0.000613
AC:
895
AN:
1460322
Hom.:
9
Cov.:
31
AF XY:
0.000527
AC XY:
383
AN XY:
726532
show subpopulations
Gnomad4 AFR exome
AF:
0.0214
Gnomad4 AMR exome
AF:
0.00116
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000812
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000234
Gnomad4 OTH exome
AF:
0.00139
GnomAD4 genome
AF:
0.00585
AC:
891
AN:
152278
Hom.:
7
Cov.:
32
AF XY:
0.00599
AC XY:
446
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0202
Gnomad4 AMR
AF:
0.00189
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.00380
Alfa
AF:
0.00271
Hom.:
2
Bravo
AF:
0.00671
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 18, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
1.2
Dann
Benign
0.54
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs142113631; hg19: chr16-57416326; API