rs12636547

Variant names:

• chr3-39275337-G-C
• rs12636547
• NM_001337.4:c.-10+4617C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-39275337-G-C
• chr3-39275337-G-T

Variant summary

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

The NM_001337.4(CX3CR1):​c.-10+4617C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,230 control chromosomes in the GnomAD database, including 450 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 0.075 (450 hom., cov: 33)
• Consequence: CX3CR1 NM_001337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CX3CR1	NM_001337.4	c.-10+4617C>G		intron_variant	Intron 1 of 1	ENST00000399220.3	NP_001328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CX3CR1	ENST00000399220.3	c.-10+4617C>G		intron_variant	Intron 1 of 1	1	NM_001337.4	ENSP00000382166.3

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11424 AN: 152112 Hom.: 451 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0751 AC: 11435 AN: 152230 Hom.: 450 Cov.: 33 AF XY: 0.0776 AC XY: 5779 AN XY: 74428

African (AFR) AF: 0.0531 AC: 2205 AN: 41534

American (AMR) AF: 0.0847 AC: 1295 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3472

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5176

South Asian (SAS) AF: 0.109 AC: 523 AN: 4820

European-Finnish (FIN) AF: 0.0984 AC: 1043 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5610 AN: 68016

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0306 Hom.: 19

Bravo AF: 0.0730

Asia WGS AF: 0.0740 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.57
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12636547; hg19: chr3-39316828;