Variant rs1801157 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

CXCL12 links:

Genome browser will be placed here

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 linkuse as main transcript	c.*519G>A		3_prime_UTR_variant	4/4		NP_000600.1
CXCL12	NM_001277990.2 linkuse as main transcript	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 linkuse as main transcript	c.*519G>A		3_prime_UTR_variant	4/4	1		ENSP00000363551	A1	P48061-1
CXCL12	ENST00000395793.7 linkuse as main transcript	c.*79G>A		3_prime_UTR_variant	3/3	5		ENSP00000379139		P48061-7

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24815

AN:

152020

Hom.:

2395

Cov.:

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.:

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.:

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: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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over