rs1719130

chr17-36088900-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002983.3(CCL3):c.189-138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,154,466 control chromosomes in the GnomAD database, including 31,079 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 0.22 (3726 hom., cov: 32)
  • Exomes 𝑓: 0.23 (27353 hom.)
• Consequence: CCL3 NM_002983.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

CCL3 (HGNC:10627): (C-C motif chemokine ligand 3) This locus represents a small inducible cytokine. The encoded protein, also known as macrophage inflammatory protein 1 alpha, plays a role in inflammatory responses through binding to the receptors CCR1, CCR4 and CCR5. Polymorphisms at this locus may be associated with both resistance and susceptibility to infection by human immunodeficiency virus type 1.[provided by RefSeq, Sep 2010]

CCL3-AS1 (HGNC:55229): (CCL3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL3	NM_002983.3	c.189-138A>G		intron_variant		ENST00000613922.2
CCL3	NR_168494.1	n.962-138A>G		intron_variant, non_coding_transcript_variant
CCL3	NR_168495.1	n.172-138A>G		intron_variant, non_coding_transcript_variant
CCL3	NR_168496.1	n.135-138A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL3	ENST00000613922.2	c.189-138A>G		intron_variant		1	NM_002983.3	P1
CCL3-AS1	ENST00000620056.4	n.390-646T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32807 AN: 152046 Hom.: 3721 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.227 AC: 227888 AN: 1002302 Hom.: 27353 AF XY: 0.229 AC XY: 118104 AN XY: 515894

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.215

Gnomad4 ASJ exome AF: 0.191

Gnomad4 EAS exome AF: 0.322

Gnomad4 SAS exome AF: 0.241

Gnomad4 FIN exome AF: 0.166

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.222

GnomAD4 genome AF: 0.216 AC: 32816 AN: 152164 Hom.: 3726 Cov.: 32 AF XY: 0.213 AC XY: 15857 AN XY: 74386

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.212

Alfa AF: 0.226 Hom.: 514

Bravo AF: 0.220

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.047
Dann	Benign	0.42

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: rs1719130; hg19: chr17-34416246;