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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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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
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
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 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
0.18
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.

Other links and lift over

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