chr17-36014382-C-G

Variant names:

• chr17-36014382-C-G
• rs771329185
• NM_005064.6:c.88G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_005064.6(CCL23):​c.88G>C​(p.Glu30Gln) 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. 12/16 in silico tools predict 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: 32)
• Consequence: CCL23 NM_005064.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

Genes affected

CCL23 (HGNC:10622): (C-C motif chemokine ligand 23) This gene is one of several chemokine genes clustered on the q-arm of chromosome 17. Chemokines form a superfamily of secreted proteins involved in immunoregulatory and inflammatory processes. The superfamily is divided into four subfamilies based on the arrangement of the N-terminal cysteine residues of the mature peptide. This chemokine, a member of the CC subfamily, displays chemotactic activity on resting T lymphocytes and monocytes, lower activity on neutrophils and no activity on activated T lymphocytes. The protein is also a strong suppressor of colony formation by a multipotential hematopoietic progenitor cell line. In addition, the product of this gene is a potent agonist of the chemokine (C-C motif) receptor 1. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12665749).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL23	NM_005064.6	c.88G>C	p.Glu30Gln	missense_variant	Exon 2 of 4	ENST00000615050.2	NP_005055.3
CCL23	NM_145898.4	c.88G>C	p.Glu30Gln	missense_variant	Exon 2 of 4		NP_665905.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL23	ENST00000615050.2	c.88G>C	p.Glu30Gln	missense_variant	Exon 2 of 4	1	NM_005064.6	ENSP00000481357.1
CCL23	ENST00000612516.4	c.88G>C	p.Glu30Gln	missense_variant	Exon 2 of 4	1		ENSP00000484748.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.1
DANN	Benign	0.97
Eigen	Benign	-0.71
Eigen_PC	Benign	-0.93
FATHMM_MKL	Benign	0.036	N
M_CAP	Benign	0.0043	T
MetaRNN	Benign	0.13	T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.23	T
Sift4G	Benign	0.23	T;T
Vest4		0.15
MutPred		0.22		Loss of ubiquitination at K25 (P = 0.092);Loss of ubiquitination at K25 (P = 0.092);
MVP		0.43
ClinPred		0.13	T
GERP RS		-1.8
gMVP		0.19

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

LitVar

Other links and lift over

dbSNP: rs771329185; hg19: chr17-34341422;