rs76444314

Variant names:

• chr10-44385008-CGCGGGCGGGCGGGCGG-C
• rs76444314
• NM_199168.4:c.-19_-4delCCGCCCGCCCGCCCGC

Your query was ambiguous. Multiple possible variants found:

• chr10-44385008-CGCGGGCGGGCGGGCGG-C
• chr10-44385008-CGCGGGCGGGCGGGCGG-CGCGG
• chr10-44385008-CGCGGGCGGGCGGGCGG-CGCGGGCGG
• chr10-44385008-CGCGGGCGGGCGGGCGG-CGCGGGCGGGCGG
• chr10-44385008-CGCGGGCGGGCGGGCGG-CGCGGGCGGGCGGGCGGGCGG
• chr10-44385008-CGCGGGCGGGCGGGCGG-CGCGGGCGGGCGGGCGGGCGGGCGG
• chr10-44385008-CGCGGGCGGGCGGGCGG-CGCGGGCGGGCGGGCGGGCGGGCGGGCGG

Variant summary

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

The NM_199168.4(CXCL12):​c.-19_-4delCCGCCCGCCCGCCCGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 412,336 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00011 (0 hom.)
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCL12	NM_199168.4	c.-19_-4delCCGCCCGCCCGCCCGC		5_prime_UTR_variant	Exon 1 of 3	ENST00000343575.11	NP_954637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCL12	ENST00000343575.11	c.-19_-4delCCGCCCGCCCGCCCGC		5_prime_UTR_variant	Exon 1 of 3	1	NM_199168.4	ENSP00000339913.6

Frequencies

GnomAD3 genomes AF: 0.0000335 AC: 4 AN: 119522 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000609

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000652

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000875 AC: 5 AN: 57116 AF XY: 0.000118

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000106 AC: 31 AN: 292782 Hom.: 0 AF XY: 0.0000937 AC XY: 15 AN XY: 160158

African (AFR) AF: 0.00 AC: 0 AN: 7744

American (AMR) AF: 0.000144 AC: 2 AN: 13850

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8866

East Asian (EAS) AF: 0.00 AC: 0 AN: 3210

South Asian (SAS) AF: 0.000169 AC: 7 AN: 41444

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9952

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1102

European-Non Finnish (NFE) AF: 0.0000980 AC: 19 AN: 193828

Other (OTH) AF: 0.000235 AC: 3 AN: 12786

GnomAD4 genome AF: 0.0000335 AC: 4 AN: 119554 Hom.: 0 Cov.: 0 AF XY: 0.0000350 AC XY: 2 AN XY: 57164

African (AFR) AF: 0.0000608 AC: 2 AN: 32870

American (AMR) AF: 0.00 AC: 0 AN: 11470

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3100

East Asian (EAS) AF: 0.00 AC: 0 AN: 3408

South Asian (SAS) AF: 0.000652 AC: 2 AN: 3066

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5434

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 246

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 57560

Other (OTH) AF: 0.00 AC: 0 AN: 1638

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3
Mutation Taster		=298/2	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs76444314; hg19: chr10-44880456;