3-39267724-C-T

Position:

• chr3-39267724-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.-9-1206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,060 control chromosomes in the GnomAD database, including 17,506 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 0.46 (17506 hom., cov: 32)
• Consequence: CX3CR1 NM_001337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CX3CR1	NM_001337.4	c.-9-1206G>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.-9-1206G>A		intron_variant		1	NM_001337.4	ENSP00000382166.3

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69974 AN: 151942 Hom.: 17510 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.460 AC: 69988 AN: 152060 Hom.: 17506 Cov.: 32 AF XY: 0.468 AC XY: 34750 AN XY: 74330

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.462

Alfa AF: 0.505 Hom.: 10070

Bravo AF: 0.448

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.017
DANN	Benign	0.40

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: rs17793056; hg19: chr3-39309215;