chr3-39276797-C-T

Variant names:

• chr3-39276797-C-T
• rs2853712
• NM_001337.4:c.-10+3157G>A

Variant summary

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

The NM_001171174.1(CX3CR1):​c.87+4812G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,980 control chromosomes in the GnomAD database, including 23,653 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 0.55 (23653 hom., cov: 32)
• Consequence: CX3CR1 NM_001171174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 8 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001171174.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CR1	NM_001337.4	MANE Select	c.-10+3157G>A		intron	N/A	NP_001328.1
	CX3CR1	NM_001171174.1		c.87+4812G>A		intron	N/A	NP_001164645.1
	CX3CR1	NM_001171171.2		c.-10+4246G>A		intron	N/A	NP_001164642.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CR1	ENST00000399220.3	TSL:1 MANE Select	c.-10+3157G>A		intron	N/A	ENSP00000382166.3
	CX3CR1	ENST00000358309.3	TSL:2	c.87+4812G>A		intron	N/A	ENSP00000351059.3
	CX3CR1	ENST00000541347.5	TSL:4	c.-10+4246G>A		intron	N/A	ENSP00000439140.1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83866 AN: 151862 Hom.: 23651 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.552 AC: 83892 AN: 151980 Hom.: 23653 Cov.: 32 AF XY: 0.556 AC XY: 41330 AN XY: 74304

African (AFR) AF: 0.460 AC: 19056 AN: 41410

American (AMR) AF: 0.637 AC: 9725 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3466

East Asian (EAS) AF: 0.822 AC: 4258 AN: 5178

South Asian (SAS) AF: 0.686 AC: 3310 AN: 4822

European-Finnish (FIN) AF: 0.571 AC: 6024 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 144 AN: 290

European-Non Finnish (NFE) AF: 0.553 AC: 37611 AN: 67974

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.553 Hom.: 42166

Bravo AF: 0.553

Asia WGS AF: 0.751 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.67
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: rs2853712; hg19: chr3-39318288;