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rs1801157

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.813
Variant links:
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 -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
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 UniProt
CXCL12NM_000609.7 linkuse as main transcriptc.*519G>A 3_prime_UTR_variant 4/4
CXCL12NM_001277990.2 linkuse as main transcriptc.*79G>A 3_prime_UTR_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CXCL12ENST00000374429.6 linkuse as main transcriptc.*519G>A 3_prime_UTR_variant 4/41 A1P48061-1
CXCL12ENST00000395793.7 linkuse as main transcriptc.*79G>A 3_prime_UTR_variant 3/35 P48061-7

Frequencies

GnomAD3 genomes
AF:
0.163
AC:
24815
AN:
152020
Hom.:
2395
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0623
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.172
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.187
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.183
GnomAD4 exome
AF:
0.195
AC:
257184
AN:
1320258
Hom.:
25890
Cov.:
35
AF XY:
0.196
AC XY:
126557
AN XY:
644322
show subpopulations
Gnomad4 AFR exome
AF:
0.0567
Gnomad4 AMR exome
AF:
0.170
Gnomad4 ASJ exome
AF:
0.225
Gnomad4 EAS exome
AF:
0.300
Gnomad4 SAS exome
AF:
0.223
Gnomad4 FIN exome
AF:
0.197
Gnomad4 NFE exome
AF:
0.193
Gnomad4 OTH exome
AF:
0.203
GnomAD4 genome
AF:
0.163
AC:
24838
AN:
152138
Hom.:
2405
Cov.:
32
AF XY:
0.165
AC XY:
12275
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0621
Gnomad4 AMR
AF:
0.173
Gnomad4 ASJ
AF:
0.233
Gnomad4 EAS
AF:
0.270
Gnomad4 SAS
AF:
0.232
Gnomad4 FIN
AF:
0.187
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.191
Alfa
AF:
0.184
Hom.:
1411
Bravo
AF:
0.157
Asia WGS
AF:
0.237
AC:
824
AN:
3478

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 submitterclinical testingGeneDxNov 12, 2018This variant is associated with the following publications: (PMID: 23325742, 19601773, 16306115, 22962615, 24361877, 23615182, 18928397, 9430590, 27832196) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
0.013
Dann
Benign
0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1801157; hg19: chr10-44868257; COSMIC: COSV59107693; COSMIC: COSV59107693; API