rs4151117

Variant names:

• chr16-57383222-G-C
• rs4151117
• NM_002996.6:c.*190G>C

Your query was ambiguous. Multiple possible variants found:

• chr16-57383222-G-C
• chr16-57383222-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002996.6(CX3CL1):​c.*190G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CX3CL1 NM_002996.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 22 publications found

Genes affected

CX3CL1 (HGNC:10647): (C-X3-C motif chemokine ligand 1) This gene belongs to the CX3C subgroup of chemokines, characterized by the number of amino acids located between the conserved cysteine residues. This is the only member of the CX3C subgroup, which contains three amino acids between cysteine residues, resulting in a Cys-X-X-X-Cys configuration. The encoded protein contains an extended mucin-like stalk with a chemokine domain on top, and exists in both a membrane-anchored form where it acts as a binding molecule, or, in soluble form, as a chemotactic cytokine. The mature form of this protein can be cleaved at the cell surface, yielding different soluble forms that can interact with the G-protein coupled receptor, C-X3-C motif chemokine receptor 1 gene product. This gene plays a role in a wide range of diseases, including cancer, vasculitis, neuropathies, atherosclerosis, inflammatory diseases, and in human immunodeficiency virus infections. [provided by RefSeq, Sep 2017]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002996.6. 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
	CX3CL1	NM_002996.6	MANE Select	c.*190G>C		3_prime_UTR	Exon 3 of 3	NP_002987.1
	CX3CL1	NM_001304392.3		c.*190G>C		3_prime_UTR	Exon 2 of 2	NP_001291321.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CL1	ENST00000006053.7	TSL:1 MANE Select	c.*190G>C		3_prime_UTR	Exon 3 of 3	ENSP00000006053.6
	CX3CL1	ENST00000565912.1	TSL:1	c.*190G>C		3_prime_UTR	Exon 2 of 2	ENSP00000464114.1
	CX3CL1	ENST00000563383.1	TSL:5	c.*190G>C		3_prime_UTR	Exon 3 of 3	ENSP00000456830.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 297476 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 150100

African (AFR) AF: 0.00 AC: 0 AN: 8210

American (AMR) AF: 0.00 AC: 0 AN: 7608

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9570

East Asian (EAS) AF: 0.00 AC: 0 AN: 23158

South Asian (SAS) AF: 0.00 AC: 0 AN: 3906

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22198

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1424

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 203460

Other (OTH) AF: 0.00 AC: 0 AN: 17942

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.015
DANN	Benign	0.46
PhyloP100		-3.0

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: rs4151117; hg19: chr16-57417134;