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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;