chr3-39270092-C-G

Position:

• chr3-39270092-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001337.4(CX3CR1):​c.-9-3574G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,230 control chromosomes in the GnomAD database, including 2,948 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 0.18 (2948 hom., cov: 33)
• Consequence: CX3CR1 NM_001337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CX3CR1	NM_001337.4	c.-9-3574G>C		intron_variant		ENST00000399220.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CX3CR1	ENST00000399220.3	c.-9-3574G>C		intron_variant		1	NM_001337.4	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27645 AN: 152112 Hom.: 2948 Cov.: 33

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.00615

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.182 AC: 27657 AN: 152230 Hom.: 2948 Cov.: 33 AF XY: 0.179 AC XY: 13343 AN XY: 74430

Gnomad4 AFR AF: 0.0992

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.00635

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.185

Alfa AF: 0.223 Hom.: 507

Bravo AF: 0.169

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.68

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: rs9862876; hg19: chr3-39311583;