rs2853707

Variant names:

• chr3-39282792-G-A
• rs2853707
• XM_047447538.1:c.-10+10000C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CX3CR1	XM_047447538.1	c.-10+10000C>T		intron_variant	Intron 1 of 1		XP_047303494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.746 AC: 30967 AN: 41512

American (AMR) AF: 0.852 AC: 13039 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2771 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4809 AN: 5186

South Asian (SAS) AF: 0.860 AC: 4149 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8240 AN: 10586

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52600 AN: 67992

Other (OTH) AF: 0.800 AC: 1691 AN: 2114

Alfa AF: 0.781 Hom.: 55252

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2853707; hg19: chr3-39324283;