rs2853711

Variant names:

• chr3-39277306-G-T
• rs2853711
• NM_001337.4:c.-10+2648C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001337.4(CX3CR1):​c.-10+2648C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,078 control chromosomes in the GnomAD database, including 5,342 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 0.26 (5342 hom., cov: 31)
• Consequence: CX3CR1 NM_001337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001337.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CR1	NM_001337.4	MANE Select	c.-10+2648C>A		intron	N/A	NP_001328.1
	CX3CR1	NM_001171174.1		c.87+4303C>A		intron	N/A	NP_001164645.1
	CX3CR1	NM_001171171.2		c.-10+3737C>A		intron	N/A	NP_001164642.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CR1	ENST00000399220.3	TSL:1 MANE Select	c.-10+2648C>A		intron	N/A	ENSP00000382166.3
	CX3CR1	ENST00000358309.3	TSL:2	c.87+4303C>A		intron	N/A	ENSP00000351059.3
	CX3CR1	ENST00000541347.5	TSL:4	c.-10+3737C>A		intron	N/A	ENSP00000439140.1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40204 AN: 151960 Hom.: 5340 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.264 AC: 40222 AN: 152078 Hom.: 5342 Cov.: 31 AF XY: 0.260 AC XY: 19358 AN XY: 74338

African (AFR) AF: 0.278 AC: 11511 AN: 41456

American (AMR) AF: 0.255 AC: 3899 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3470

East Asian (EAS) AF: 0.150 AC: 777 AN: 5180

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4816

European-Finnish (FIN) AF: 0.219 AC: 2316 AN: 10592

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18512 AN: 67964

Other (OTH) AF: 0.240 AC: 505 AN: 2108

Alfa AF: 0.272 Hom.: 8085

Bravo AF: 0.266

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.85
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2853711; hg19: chr3-39318797;