10-44385008-CGCGGGCGGGCGGGCGG-CGCGG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_199168.4(CXCL12):c.-15_-4del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000324 in 410,968 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00018 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00038 (2 hom.)
• Consequence: CXCL12 NM_199168.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.28

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXCL12	NM_199168.4	c.-15_-4del		5_prime_UTR_variant	1/3	ENST00000343575.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXCL12	ENST00000343575.11	c.-15_-4del		5_prime_UTR_variant	1/3	1	NM_199168.4	P4

Frequencies

GnomAD3 genomes AF: 0.000176 AC: 21 AN: 119512 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000518

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000874

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000184

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000347

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000263 AC: 15 AN: 57116 Hom.: 1 AF XY: 0.000266 AC XY: 9 AN XY: 33858

Gnomad AFR exome AF: 0.00325

Gnomad AMR exome AF: 0.000254

Gnomad ASJ exome AF: 0.000204

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000388

Gnomad FIN exome AF: 0.000583

Gnomad NFE exome AF: 0.0000845

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000384 AC: 112 AN: 291456 Hom.: 2 AF XY: 0.000345 AC XY: 55 AN XY: 159454

Gnomad4 AFR exome AF: 0.00233

Gnomad4 AMR exome AF: 0.000363

Gnomad4 ASJ exome AF: 0.000226

Gnomad4 EAS exome AF: 0.000937

Gnomad4 SAS exome AF: 0.000411

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000327

Gnomad4 OTH exome AF: 0.000314

GnomAD4 genome AF: 0.000176 AC: 21 AN: 119512 Hom.: 0 Cov.: 0 AF XY: 0.000158 AC XY: 9 AN XY: 57134

Gnomad4 AFR AF: 0.000518

Gnomad4 AMR AF: 0.0000874

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000184

Gnomad4 NFE AF: 0.0000347

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76444314; hg19: chr10-44880456;