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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.813

Links

CXCL12 (HGNC:10672):

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 linkuse as main transcript	c.*519G>A		3_prime_UTR_variant	4/4
CXCL12	NM_001277990.2 linkuse as main transcript	c.*79G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXCL12	ENST00000374429.6 linkuse as main transcript	c.*519G>A		3_prime_UTR_variant	4/4	1		A1	P48061-1
CXCL12	ENST00000395793.7 linkuse as main transcript	c.*79G>A		3_prime_UTR_variant	3/3	5			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

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

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 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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

Cadd

Benign

0.18

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over