chr17-34287406-G-A

Variant names:

• chr17-34287406-G-A
• rs3815341
• NM_002986.3:c.189-179G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002986.3(CCL11):​c.189-179G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.043 in 152,186 control chromosomes in the GnomAD database, including 275 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 0.043 (275 hom., cov: 32)
• Consequence: CCL11 NM_002986.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 8 publications found

Genes affected

CCL11 (HGNC:10610): (C-C motif chemokine ligand 11) This antimicrobial 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 for eosinophils, but not mononuclear cells or neutrophils. This eosinophil-specific chemokine is thought to be involved in eosinophilic inflammatory diseases such as atopic dermatitis, allergic rhinitis, asthma and parasitic infections. [provided by RefSeq, Sep 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002986.3. 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
	CCL11	NM_002986.3	MANE Select	c.189-179G>A		intron	N/A	NP_002977.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL11	ENST00000305869.4	TSL:1 MANE Select	c.189-179G>A		intron	N/A	ENSP00000302234.3

Frequencies

GnomAD3 genomes AF: 0.0430 AC: 6534 AN: 152068 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0455

Gnomad OTH AF: 0.0441

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0430 AC: 6544 AN: 152186 Hom.: 275 Cov.: 32 AF XY: 0.0465 AC XY: 3460 AN XY: 74390

African (AFR) AF: 0.0103 AC: 428 AN: 41542

American (AMR) AF: 0.0412 AC: 630 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3472

East Asian (EAS) AF: 0.0898 AC: 465 AN: 5178

South Asian (SAS) AF: 0.214 AC: 1027 AN: 4810

European-Finnish (FIN) AF: 0.0526 AC: 557 AN: 10588

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3091 AN: 67996

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0541 Hom.: 192

Bravo AF: 0.0368

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.74
PhyloP100		-0.062
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3815341; hg19: chr17-32614425;