rs1910383284

Variant names:

• chr17-34357562-C-A
• rs1910383284
• NM_005408.3:c.164C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-34357562-C-A
• chr17-34357562-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005408.3(CCL13):​c.164C>A​(p.Thr55Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCL13 NM_005408.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.241
• Publications: 0 publications found

Genes affected

CCL13 (HGNC:10611): (C-C motif chemokine ligand 13) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for monocytes, lymphocytes, basophils and eosinophils, but not neutrophils. This chemokine plays a role in accumulation of leukocytes during inflammation. It may also be involved in the recruitment of monocytes into the arterial wall during artherosclerosis. [provided by RefSeq, Sep 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05821246).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005408.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL13	NM_005408.3	MANE Select	c.164C>A	p.Thr55Asn	missense	Exon 2 of 3	NP_005399.1	Q99616

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL13	ENST00000225844.7	TSL:1 MANE Select	c.164C>A	p.Thr55Asn	missense	Exon 2 of 3	ENSP00000225844.2	Q99616
	CCL13	ENST00000577681.1	TSL:1	c.77C>A	p.Thr26Asn	missense	Exon 1 of 2	ENSP00000463667.1	J3QLQ9

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.053
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.64
DANN	Benign	0.41
DEOGEN2	Benign	0.060	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.017	N
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.0052	T
MetaRNN	Benign	0.058	T
MetaSVM	Benign	-0.93	T
PhyloP100		-0.24
PrimateAI	Benign	0.33	T
PROVEAN	Benign	0.97	N
REVEL	Benign	0.015
Sift	Benign	0.30	T
Sift4G	Benign	0.24	T
Polyphen		0.0	B
Vest4		0.15
MutPred		0.47		Loss of MoRF binding (P = 0.1378)
MVP		0.15
MPC		0.12
ClinPred		0.057	T
GERP RS		-4.1
PromoterAI		-0.016	Neutral
Varity_R		0.24
gMVP		0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1910383284; hg19: chr17-32684581;