chr5-135571862-G-A

Variant names:

• chr5-135571862-G-A
• rs2547
• NM_004887.5:c.291C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_004887.5(CXCL14):​c.291C>T​(p.Tyr97Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 1,582,688 control chromosomes in the GnomAD database, including 6,958 homozygotes. 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: 𝑓 0.088 (498 hom., cov: 29)
  • Exomes 𝑓: 0.091 (6460 hom.)
• Consequence: CXCL14 NM_004887.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 17 publications found

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]

ENSG00000250167 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP7: Synonymous conserved (PhyloP=0.132 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004887.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL14	NM_004887.5	MANE Select	c.291C>T	p.Tyr97Tyr	synonymous	Exon 4 of 4	NP_004878.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL14	ENST00000512158.6	TSL:1 MANE Select	c.291C>T	p.Tyr97Tyr	synonymous	Exon 4 of 4	ENSP00000423783.1
	CXCL14	ENST00000337225.5	TSL:1	c.327C>T	p.Tyr109Tyr	synonymous	Exon 4 of 4	ENSP00000337065.5
	ENSG00000250167	ENST00000509372.1	TSL:3	n.74+12212G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 12509 AN: 141930 Hom.: 497 Cov.: 29

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.0290

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0892

GnomAD2 exomes AF: 0.0885 AC: 22177 AN: 250638 AF XY: 0.0932

Gnomad AFR exome AF: 0.0822

Gnomad AMR exome AF: 0.0415

Gnomad ASJ exome AF: 0.113

Gnomad EAS exome AF: 0.105

Gnomad FIN exome AF: 0.0621

Gnomad NFE exome AF: 0.0847

Gnomad OTH exome AF: 0.0826

GnomAD4 exome AF: 0.0908 AC: 130834 AN: 1440666 Hom.: 6460 Cov.: 32 AF XY: 0.0934 AC XY: 66901 AN XY: 716630

African (AFR) AF: 0.0808 AC: 2640 AN: 32678

American (AMR) AF: 0.0434 AC: 1906 AN: 43880

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 3013 AN: 25498

East Asian (EAS) AF: 0.0851 AC: 3252 AN: 38200

South Asian (SAS) AF: 0.156 AC: 13399 AN: 85870

European-Finnish (FIN) AF: 0.0646 AC: 3343 AN: 51714

Middle Eastern (MID) AF: 0.0806 AC: 458 AN: 5680

European-Non Finnish (NFE) AF: 0.0883 AC: 96913 AN: 1098138

Other (OTH) AF: 0.100 AC: 5910 AN: 59008

GnomAD4 genome AF: 0.0882 AC: 12523 AN: 142022 Hom.: 498 Cov.: 29 AF XY: 0.0894 AC XY: 6102 AN XY: 68284

African (AFR) AF: 0.0877 AC: 3319 AN: 37834

American (AMR) AF: 0.0673 AC: 886 AN: 13168

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 443 AN: 3436

East Asian (EAS) AF: 0.116 AC: 544 AN: 4696

South Asian (SAS) AF: 0.163 AC: 730 AN: 4478

European-Finnish (FIN) AF: 0.0737 AC: 646 AN: 8760

Middle Eastern (MID) AF: 0.106 AC: 27 AN: 254

European-Non Finnish (NFE) AF: 0.0861 AC: 5731 AN: 66562

Other (OTH) AF: 0.0883 AC: 171 AN: 1936

Alfa AF: 0.0825 Hom.: 1405

Bravo AF: 0.0809

Asia WGS AF: 0.117 AC: 411 AN: 3478

EpiCase AF: 0.0886

EpiControl AF: 0.0900

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	5.2
DANN	Benign	0.87
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.19		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2547; hg19: chr5-134907552;