chr3-39265671-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001337.4(CX3CR1):c.839C>T(p.Thr280Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,613,948 control chromosomes in the GnomAD database, including 21,070 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).
Frequency
Genomes: 𝑓 0.12 ( 1435 hom., cov: 32)
Exomes 𝑓: 0.16 ( 19635 hom. )
Consequence
CX3CR1
NM_001337.4 missense
NM_001337.4 missense
Scores
7
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.89
Genes affected
CX3CR1 (HGNC:2558): (C-X3-C motif chemokine receptor 1) Fractalkine is a transmembrane protein and chemokine involved in the adhesion and migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. The encoded protein also is a coreceptor for HIV-1, and some variations in this gene lead to increased susceptibility to HIV-1 infection and rapid progression to AIDS. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0025131404).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CX3CR1 | NM_001337.4 | c.839C>T | p.Thr280Met | missense_variant | 2/2 | ENST00000399220.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CX3CR1 | ENST00000399220.3 | c.839C>T | p.Thr280Met | missense_variant | 2/2 | 1 | NM_001337.4 | P1 | |
CX3CR1 | ENST00000358309.3 | c.935C>T | p.Thr312Met | missense_variant | 2/2 | 2 | |||
CX3CR1 | ENST00000541347.5 | c.839C>T | p.Thr280Met | missense_variant | 2/2 | 4 | P1 | ||
CX3CR1 | ENST00000542107.5 | c.839C>T | p.Thr280Met | missense_variant | 2/2 | 4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.121 AC: 18378AN: 152028Hom.: 1431 Cov.: 32
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GnomAD3 exomes AF: 0.140 AC: 34826AN: 249502Hom.: 2881 AF XY: 0.139 AC XY: 18822AN XY: 135368
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GnomAD4 exome AF: 0.159 AC: 232796AN: 1461802Hom.: 19635 Cov.: 33 AF XY: 0.158 AC XY: 114842AN XY: 727212
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GnomAD4 genome AF: 0.121 AC: 18394AN: 152146Hom.: 1435 Cov.: 32 AF XY: 0.120 AC XY: 8947AN XY: 74372
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685
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
.;D;.;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;.
MutationTaster
Benign
P;P;P;P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;T
Sift4G
Uncertain
D;D;D;D
Polyphen
P;P;P;.
Vest4
MPC
0.46
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at