chr3-39289016-T-C

Variant names:

• chr3-39289016-T-C
• rs3020452
• XM_047447538.1:c.-10+3776A>G

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+3776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,838 control chromosomes in the GnomAD database, including 33,522 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 0.66 (33522 hom., cov: 30)
• Consequence: CX3CR1 XM_047447538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.662 AC: 100380 AN: 151720 Hom.: 33488 Cov.: 30

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.662 AC: 100466 AN: 151838 Hom.: 33522 Cov.: 30 AF XY: 0.668 AC XY: 49590 AN XY: 74190

African (AFR) AF: 0.645 AC: 26694 AN: 41398

American (AMR) AF: 0.750 AC: 11463 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2184 AN: 3464

East Asian (EAS) AF: 0.852 AC: 4387 AN: 5152

South Asian (SAS) AF: 0.757 AC: 3641 AN: 4810

European-Finnish (FIN) AF: 0.654 AC: 6881 AN: 10516

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42980 AN: 67918

Other (OTH) AF: 0.684 AC: 1436 AN: 2100

Alfa AF: 0.625 Hom.: 3883

Bravo AF: 0.668

Asia WGS AF: 0.821 AC: 2857 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.11
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs3020452; hg19: chr3-39330507;