NM_199168.4:c.-11_-4delCCGCCCGC

Variant names:

• chr10-44385006-GGCGCGGGC-GGC
• NM_199168.4:c.-9_-4delGCCCGC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_199168.4(CXCL12):​c.-9_-4delGCCCGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: CXCL12 NM_199168.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.28
• Publications: 0 publications found

Genes affected

CXCL12 (HGNC:10672): (C-X-C motif chemokine ligand 12) This antimicrobial gene encodes a stromal cell-derived alpha chemokine member of the intercrine family. The encoded protein functions as the ligand for the G-protein coupled receptor, chemokine (C-X-C motif) receptor 4, and plays a role in many diverse cellular functions, including embryogenesis, immune surveillance, inflammation response, tissue homeostasis, and tumor growth and metastasis. Mutations in this gene are associated with resistance to human immunodeficiency virus type 1 infections. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ENSG00000303087 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199168.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL12	NM_199168.4	MANE Select	c.-9_-4delGCCCGC		5_prime_UTR	Exon 1 of 3	NP_954637.1	P48061-2
	CXCL12	NM_001178134.2		c.-9_-4delGCCCGC		5_prime_UTR	Exon 1 of 4	NP_001171605.1	P48061-4
	CXCL12	NM_001033886.2		c.-9_-4delGCCCGC		5_prime_UTR	Exon 1 of 4	NP_001029058.1	P48061-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL12	ENST00000343575.11	TSL:1 MANE Select	c.-9_-4delGCCCGC		5_prime_UTR	Exon 1 of 3	ENSP00000339913.6	P48061-2
	CXCL12	ENST00000395794.2	TSL:1	c.-9_-4delGCCCGC		5_prime_UTR	Exon 1 of 4	ENSP00000379140.2	P48061-4
	CXCL12	ENST00000374426.6	TSL:1	c.-9_-4delGCCCGC		5_prime_UTR	Exon 1 of 4	ENSP00000363548.2	P48061-3

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-44880454;