NM_001337.4:c.*1629G>A

Variant names:

• chr3-39263813-C-T
• rs17038663
• NM_001337.4:c.*1629G>A

Variant summary

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

The NM_001337.4(CX3CR1):​c.*1629G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 152,276 control chromosomes in the GnomAD database, including 260 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 0.057 (260 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: CX3CR1 NM_001337.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CX3CR1	NM_001337.4	c.*1629G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000399220.3	NP_001328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CX3CR1	ENST00000399220.3	c.*1629G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_001337.4	ENSP00000382166.3
CX3CR1	ENST00000358309.3	c.*1629G>A		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000351059.3
CX3CR1	ENST00000541347.5	c.*1629G>A		3_prime_UTR_variant	Exon 2 of 2	4		ENSP00000439140.1
CX3CR1	ENST00000542107.5	c.*1629G>A		3_prime_UTR_variant	Exon 2 of 2	4		ENSP00000444928.1

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8648 AN: 152158 Hom.: 257 Cov.: 33

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0450

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0647

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0569 AC: 8663 AN: 152276 Hom.: 260 Cov.: 33 AF XY: 0.0544 AC XY: 4047 AN XY: 74454

African (AFR) AF: 0.0807 AC: 3351 AN: 41546

American (AMR) AF: 0.0449 AC: 687 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0519 AC: 251 AN: 4832

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0551 AC: 3748 AN: 68024

Other (OTH) AF: 0.0640 AC: 135 AN: 2110

Alfa AF: 0.0593 Hom.: 419

Bravo AF: 0.0606

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.66
PhyloP100		-1.8
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: rs17038663; hg19: chr3-39305304;