chr3-39284792-T-G

Variant names:

• chr3-39284792-T-G
• rs1014638
• XM_047447538.1:c.-10+8000A>C

Variant summary

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

The XM_047447538.1(CX3CR1):​c.-10+8000A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,930 control chromosomes in the GnomAD database, including 7,591 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 0.28 (7591 hom., cov: 32)
• Consequence: CX3CR1 XM_047447538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43214 AN: 151814 Hom.: 7592 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.284 AC: 43209 AN: 151930 Hom.: 7591 Cov.: 32 AF XY: 0.297 AC XY: 22066 AN XY: 74260

African (AFR) AF: 0.129 AC: 5360 AN: 41444

American (AMR) AF: 0.426 AC: 6499 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3470

East Asian (EAS) AF: 0.714 AC: 3690 AN: 5166

South Asian (SAS) AF: 0.523 AC: 2514 AN: 4806

European-Finnish (FIN) AF: 0.385 AC: 4046 AN: 10520

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19211 AN: 67940

Other (OTH) AF: 0.286 AC: 602 AN: 2108

Alfa AF: 0.274 Hom.: 3606

Bravo AF: 0.280

Asia WGS AF: 0.598 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.83
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1014638; hg19: chr3-39326283;