chr16-57376022-T-G

Variant names:

• chr16-57376022-T-G
• rs170364
• NM_002996.6:c.70+3384T>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002996.6(CX3CL1):​c.70+3384T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,132 control chromosomes in the GnomAD database, including 41,405 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.74 (41405 hom., cov: 32)
• Consequence: CX3CL1 NM_002996.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.635
• Publications: 16 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: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 16-57376022-T-G is Benign according to our data. Variant chr16-57376022-T-G is described in ClinVar as Benign. ClinVar VariationId is 1259556.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

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.70+3384T>G		intron	N/A	NP_002987.1
	CX3CL1	NM_001304392.3		c.-65+3384T>G		intron	N/A	NP_001291321.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CL1	ENST00000006053.7	TSL:1 MANE Select	c.70+3384T>G		intron	N/A	ENSP00000006053.6
	CX3CL1	ENST00000563383.1	TSL:5	c.70+3384T>G		intron	N/A	ENSP00000456830.1
	CX3CL1	ENST00000564948.1	TSL:3	c.70+3384T>G		intron	N/A	ENSP00000457996.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112014 AN: 152014 Hom.: 41377 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.737 AC: 112099 AN: 152132 Hom.: 41405 Cov.: 32 AF XY: 0.738 AC XY: 54868 AN XY: 74382

African (AFR) AF: 0.699 AC: 28980 AN: 41488

American (AMR) AF: 0.700 AC: 10693 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2585 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3753 AN: 5168

South Asian (SAS) AF: 0.679 AC: 3272 AN: 4818

European-Finnish (FIN) AF: 0.832 AC: 8826 AN: 10608

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51497 AN: 67978

Other (OTH) AF: 0.742 AC: 1565 AN: 2110

Alfa AF: 0.745 Hom.: 30599

Bravo AF: 0.724

Asia WGS AF: 0.712 AC: 2476 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 15, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 32234515)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.69
PhyloP100		-0.64
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: rs170364; hg19: chr16-57409934;