3-39281672-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001171174.1(CX3CR1):​c.24T>A​(p.Phe8Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,446,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

CX3CR1
NM_001171174.1 missense

Scores

15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13
Variant links:
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06783414).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CX3CR1NM_001171174.1 linkuse as main transcriptc.24T>A p.Phe8Leu missense_variant 1/2
CX3CR1XM_047447538.1 linkuse as main transcriptc.-10+11120T>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CX3CR1ENST00000358309.3 linkuse as main transcriptc.24T>A p.Phe8Leu missense_variant 1/22 P49238-4

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000138
AC:
2
AN:
1446464
Hom.:
0
Cov.:
37
AF XY:
0.00000278
AC XY:
2
AN XY:
719856
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
0.43
DANN
Benign
0.71
Eigen
Benign
-0.96
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.0069
N
LIST_S2
Benign
0.29
T
M_CAP
Benign
0.0072
T
MetaRNN
Benign
0.068
T
MetaSVM
Benign
-0.97
T
MutationTaster
Benign
1.0
P
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-0.040
N
REVEL
Benign
0.033
Sift
Benign
0.86
T
Vest4
0.041
MutPred
0.28
Gain of ubiquitination at K9 (P = 0.0396);
MVP
0.45
MPC
0.32
ClinPred
0.025
T
GERP RS
-2.4
gMVP
0.31

Splicing

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: rs11715522; hg19: chr3-39323163; API