rs1719130

Variant names:

• chr17-36088900-T-C
• rs1719130
• NM_002983.3:c.189-138A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCL3	NM_002983.3	c.189-138A>G		intron_variant	Intron 2 of 2	ENST00000613922.2	NP_002974.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL3	ENST00000613922.2	c.189-138A>G		intron_variant	Intron 2 of 2	1	NM_002983.3	ENSP00000477908.1

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

African (AFR) AF: 0.168 AC: 4086 AN: 24278

American (AMR) AF: 0.215 AC: 8490 AN: 39484

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 4387 AN: 22970

East Asian (EAS) AF: 0.322 AC: 11672 AN: 36252

South Asian (SAS) AF: 0.241 AC: 18168 AN: 75542

European-Finnish (FIN) AF: 0.166 AC: 8602 AN: 51806

Middle Eastern (MID) AF: 0.205 AC: 702 AN: 3430

European-Non Finnish (NFE) AF: 0.230 AC: 161798 AN: 703672

Other (OTH) AF: 0.222 AC: 9983 AN: 44868

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

African (AFR) AF: 0.175 AC: 7265 AN: 41512

American (AMR) AF: 0.204 AC: 3121 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1783 AN: 5164

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4820

European-Finnish (FIN) AF: 0.156 AC: 1658 AN: 10610

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16345 AN: 67982

Other (OTH) AF: 0.212 AC: 447 AN: 2112

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
PhyloP100		-0.42
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: rs1719130; hg19: chr17-34416246;