rs2853707

Positions:

• chr3-39282792-G-A
• chr3-39282792-G-C
• chr3-39282792-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047447538.1(CX3CR1):​c.-10+10000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,188 control chromosomes in the GnomAD database, including 46,811 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (46811 hom., cov: 32)
• Consequence: CX3CR1 XM_047447538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CX3CR1	XM_047447538.1	c.-10+10000C>T		intron_variant			XP_047303494.1
		n.39282792G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119073 AN: 152070 Hom.: 46789 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.798

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.783 AC: 119142 AN: 152188 Hom.: 46811 Cov.: 32 AF XY: 0.787 AC XY: 58533 AN XY: 74408

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.800

Alfa AF: 0.781 Hom.: 40880

Bravo AF: 0.787

Asia WGS AF: 0.882 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2853707; hg19: chr3-39324283;