rs1801157
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000374429.6(CXCL12):c.*519G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,472,396 control chromosomes in the GnomAD database, including 28,295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2405 hom., cov: 32)
Exomes 𝑓: 0.19 ( 25890 hom. )
Consequence
CXCL12
ENST00000374429.6 3_prime_UTR
ENST00000374429.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.813
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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 10-44372809-C-T is Benign according to our data. Variant chr10-44372809-C-T is described in ClinVar as [Benign]. Clinvar id is 1291069.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CXCL12 | NM_000609.7 | c.*519G>A | 3_prime_UTR_variant | 4/4 | NP_000600.1 | |||
CXCL12 | NM_001277990.2 | c.*79G>A | 3_prime_UTR_variant | 3/3 | NP_001264919.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CXCL12 | ENST00000374429.6 | c.*519G>A | 3_prime_UTR_variant | 4/4 | 1 | ENSP00000363551 | A1 | |||
CXCL12 | ENST00000395793.7 | c.*79G>A | 3_prime_UTR_variant | 3/3 | 5 | ENSP00000379139 |
Frequencies
GnomAD3 genomes AF: 0.163 AC: 24815AN: 152020Hom.: 2395 Cov.: 32
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GnomAD4 exome AF: 0.195 AC: 257184AN: 1320258Hom.: 25890 Cov.: 35 AF XY: 0.196 AC XY: 126557AN XY: 644322
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GnomAD4 genome AF: 0.163 AC: 24838AN: 152138Hom.: 2405 Cov.: 32 AF XY: 0.165 AC XY: 12275AN XY: 74378
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 23325742, 19601773, 16306115, 22962615, 24361877, 23615182, 18928397, 9430590, 27832196) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at