rs3780891
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_199168.4(CXCL12):c.61+1680C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,238 control chromosomes in the GnomAD database, including 487 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.075 ( 487 hom., cov: 32)
Consequence
CXCL12
NM_199168.4 intron
NM_199168.4 intron
Scores
2
Splicing: ADA: 0.00005694
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0610
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0947 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL12 | NM_199168.4 | c.61+1680C>T | intron_variant | ENST00000343575.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL12 | ENST00000343575.11 | c.61+1680C>T | intron_variant | 1 | NM_199168.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0755 AC: 11482AN: 152120Hom.: 488 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.114 AC: 5AN: 44Hom.: 0 AF XY: 0.0625 AC XY: 1AN XY: 16
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GnomAD4 genome ? AF: 0.0754 AC: 11480AN: 152238Hom.: 487 Cov.: 32 AF XY: 0.0750 AC XY: 5580AN XY: 74448
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3478
ClinVar
Not reported inComputational 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
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at