rs5029410

Variant names:

• chr17-36088805-A-C
• rs5029410
• NM_002983.3:c.189-43T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-36088805-A-C
• chr17-36088805-A-T

Variant summary

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

The NM_002983.3(CCL3):​c.189-43T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00511 in 1,610,366 control chromosomes in the GnomAD database, including 270 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 0.024 (131 hom., cov: 32)
  • Exomes 𝑓: 0.0032 (139 hom.)
• Consequence: CCL3 NM_002983.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002983.3. 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
	CCL3	NM_002983.3	MANE Select	c.189-43T>G		intron	N/A	NP_002974.1	P10147
	CCL3	NR_168494.1		n.962-43T>G		intron	N/A
	CCL3	NR_168495.1		n.172-43T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL3	ENST00000613922.2	TSL:1 MANE Select	c.189-43T>G		intron	N/A	ENSP00000477908.1	P10147
	CCL3	ENST00000614051.1	TSL:1	n.988-43T>G		intron	N/A
	CCL3	ENST00000613928.1	TSL:5	n.804-199T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3610 AN: 152178 Hom.: 129 Cov.: 32

Gnomad AFR AF: 0.0805

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000764

Gnomad OTH AF: 0.0205

GnomAD2 exomes AF: 0.00750 AC: 1879 AN: 250692 AF XY: 0.00590

Gnomad AFR exome AF: 0.0846

Gnomad AMR exome AF: 0.00784

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.000218

Gnomad FIN exome AF: 0.0000924

Gnomad NFE exome AF: 0.000486

Gnomad OTH exome AF: 0.00507

GnomAD4 exome AF: 0.00316 AC: 4606 AN: 1458070 Hom.: 139 Cov.: 29 AF XY: 0.00302 AC XY: 2193 AN XY: 725562

African (AFR) AF: 0.0853 AC: 2848 AN: 33382

American (AMR) AF: 0.00837 AC: 374 AN: 44702

Ashkenazi Jewish (ASJ) AF: 0.000153 AC: 4 AN: 26104

East Asian (EAS) AF: 0.000126 AC: 5 AN: 39688

South Asian (SAS) AF: 0.00443 AC: 382 AN: 86184

European-Finnish (FIN) AF: 0.0000936 AC: 5 AN: 53398

Middle Eastern (MID) AF: 0.00548 AC: 31 AN: 5652

European-Non Finnish (NFE) AF: 0.000523 AC: 580 AN: 1108724

Other (OTH) AF: 0.00626 AC: 377 AN: 60236

GnomAD4 genome AF: 0.0238 AC: 3623 AN: 152296 Hom.: 131 Cov.: 32 AF XY: 0.0233 AC XY: 1736 AN XY: 74488

African (AFR) AF: 0.0805 AC: 3346 AN: 41550

American (AMR) AF: 0.0103 AC: 157 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.000289 AC: 1 AN: 3462

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.00415 AC: 20 AN: 4824

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000764 AC: 52 AN: 68024

Other (OTH) AF: 0.0203 AC: 43 AN: 2116

Alfa AF: 0.0101 Hom.: 11

Bravo AF: 0.0275

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.75
PhyloP100		0.0030
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: rs5029410; hg19: chr17-34416151;