GeneBe

rs1277526581

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_004887.5(CXCL14):​c.19G>T​(p.Ala7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000717 in 1,393,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

CXCL14
NM_004887.5 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.99
Variant links:
Genes affected
CXCL14 (HGNC:10640): (C-X-C motif chemokine ligand 14) This antimicrobial gene belongs to the cytokine gene family which encode secreted proteins involved in immunoregulatory and inflammatory processes. The protein encoded by this gene is structurally related to the CXC (Cys-X-Cys) subfamily of cytokines. Members of this subfamily are characterized by two cysteines separated by a single amino acid. This cytokine displays chemotactic activity for monocytes but not for lymphocytes, dendritic cells, neutrophils or macrophages. It has been implicated that this cytokine is involved in the homeostasis of monocyte-derived macrophages rather than in inflammation. [provided by RefSeq, Sep 2014]
SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30112627).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CXCL14NM_004887.5 linkc.19G>T p.Ala7Ser missense_variant Exon 1 of 4 ENST00000512158.6 NP_004878.3 O95715

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CXCL14ENST00000512158.6 linkc.19G>T p.Ala7Ser missense_variant Exon 1 of 4 1 NM_004887.5 ENSP00000423783.1 A0A0C4DGC1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
7.17e-7
AC:
1
AN:
1393896
Hom.:
0
Cov.:
31
AF XY:
0.00000145
AC XY:
1
AN XY:
687704
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.28e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.072
T
BayesDel_noAF
Benign
-0.34
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.034
T;T
Eigen
Uncertain
0.25
Eigen_PC
Uncertain
0.30
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Benign
0.61
T;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.30
T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
1.5
.;L
PrimateAI
Uncertain
0.75
T
PROVEAN
Benign
-2.2
N;N
REVEL
Benign
0.040
Sift
Benign
0.030
D;D
Sift4G
Uncertain
0.014
D;D
Polyphen
0.81
.;P
Vest4
0.49
MutPred
0.37
.;Gain of disorder (P = 0.0447);
MVP
0.63
MPC
1.3
ClinPred
0.93
D
GERP RS
3.7
Varity_R
0.25
gMVP
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-134914450; API