chr3-39277306-G-T

Position:

• chr3-39277306-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CX3CR1	NM_001337.4	c.-10+2648C>A		intron_variant		ENST00000399220.3	NP_001328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CX3CR1	ENST00000399220.3	c.-10+2648C>A		intron_variant		1	NM_001337.4	ENSP00000382166.3

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.240

Alfa AF: 0.273 Hom.: 4802

Bravo AF: 0.266

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.85

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853711; hg19: chr3-39318797;