rs1801157
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000374429(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 0.163 in 152020 control chromosomes in the gnomAD Genomes database, including 2395 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2395 hom., cov: 32)
Consequence
CXCL12
ENST00000374429 3_prime_UTR
ENST00000374429 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.813
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 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_single_submitter, 1 stars.
BA1
?
GnomAd 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 | UniProt |
---|---|---|---|---|---|---|---|
CXCL12 | NM_000609.7 | c.*519G>A | 3_prime_UTR_variant | 4/4 | |||
CXCL12 | NM_001277990.2 | c.*79G>A | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL12 | ENST00000374429.6 | c.*519G>A | 3_prime_UTR_variant | 4/4 | 1 | A1 | |||
CXCL12 | ENST00000395793.7 | c.*79G>A | 3_prime_UTR_variant | 3/3 | 5 |
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 AF XY: 0.196 AC XY: 126557AN XY: 644322
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
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) - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at