rs2853712

chr3-39276797-C-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+3157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,980 control chromosomes in the GnomAD database, including 23,653 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 0.55 (23653 hom., cov: 32)
• Consequence: CX3CR1 NM_001337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CX3CR1	NM_001337.4	c.-10+3157G>A		intron_variant		ENST00000399220.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CX3CR1	ENST00000399220.3	c.-10+3157G>A		intron_variant		1	NM_001337.4	P1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83866 AN: 151862 Hom.: 23651 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.552 AC: 83892 AN: 151980 Hom.: 23653 Cov.: 32 AF XY: 0.556 AC XY: 41330 AN XY: 74304

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.551

Alfa AF: 0.557 Hom.: 23434

Bravo AF: 0.553

Asia WGS AF: 0.751 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	11
Dann	Benign	0.67

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: rs2853712; hg19: chr3-39318288;