chr10-44373096-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The ENST00000374429.6(CXCL12):c.*232A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00294 in 1,536,422 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0023 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 7 hom. )
Consequence
CXCL12
ENST00000374429.6 3_prime_UTR
ENST00000374429.6 3_prime_UTR
Scores
2
Splicing: ADA: 0.00003135
2
Clinical Significance
Conservation
PhyloP100: -0.397
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 Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 10-44373096-T-C is Benign according to our data. Variant chr10-44373096-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3037442.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL12 | NM_000609.7 | c.*232A>G | 3_prime_UTR_variant | 4/4 | |||
CXCL12 | NM_001277990.2 | c.110-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL12 | ENST00000374429.6 | c.*232A>G | 3_prime_UTR_variant | 4/4 | 1 | A1 | |||
CXCL12 | ENST00000395793.7 | c.110-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00235 AC: 358AN: 152250Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00222 AC: 310AN: 139700Hom.: 0 AF XY: 0.00242 AC XY: 182AN XY: 75314
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GnomAD4 exome AF: 0.00301 AC: 4161AN: 1384054Hom.: 7 Cov.: 34 AF XY: 0.00302 AC XY: 2065AN XY: 682800
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CXCL12-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 19, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
Find out detailed SpliceAI scores and Pangolin per-transcript scores at