chr10-44385008-C-CGCGGGCGGGCGG
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_199168.4(CXCL12):c.-4_-3insCCGCCCGCCCGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 293,020 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000020 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CXCL12
NM_199168.4 5_prime_UTR
NM_199168.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.689
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]
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ACMG classification
Classification made for transcript
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.-4_-3insCCGCCCGCCCGC | 5_prime_UTR_variant | 1/3 | ENST00000343575.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL12 | ENST00000343575.11 | c.-4_-3insCCGCCCGCCCGC | 5_prime_UTR_variant | 1/3 | 1 | NM_199168.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 7AN: 119524Hom.: 0 Cov.: 28 FAILED QC
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GnomAD4 exome AF: 0.0000205 AC: 6AN: 293020Hom.: 0 Cov.: 32 AF XY: 0.00000624 AC XY: 1AN XY: 160284
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000586 AC: 7AN: 119524Hom.: 0 Cov.: 28 AF XY: 0.0000700 AC XY: 4AN XY: 57140
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at