rs1719134

Positions:

• chr17-36089600-G-A
• chr17-36089600-G-C

Variant summary

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

The NM_002983.3(CCL3):​c.74-303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 606,860 control chromosomes in the GnomAD database, including 16,281 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 0.20 (3380 hom., cov: 31)
  • Exomes 𝑓: 0.23 (12901 hom.)
• Consequence: CCL3 NM_002983.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCL3	NM_002983.3	c.74-303C>T		intron_variant		ENST00000613922.2	NP_002974.1
CCL3	NR_168494.1	n.544C>T		non_coding_transcript_exon_variant	1/2
CCL3	NR_168495.1	n.56+198C>T		intron_variant, non_coding_transcript_variant
CCL3	NR_168496.1	n.19+80C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL3	ENST00000613922.2	c.74-303C>T		intron_variant		1	NM_002983.3	ENSP00000477908	P1
CCL3-AS1	ENST00000620056.4	n.444G>A		non_coding_transcript_exon_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30883 AN: 151946 Hom.: 3376 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.233 AC: 105902 AN: 454796 Hom.: 12901 Cov.: 3 AF XY: 0.234 AC XY: 57408 AN XY: 245696

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.207

Gnomad4 ASJ exome AF: 0.194

Gnomad4 EAS exome AF: 0.322

Gnomad4 SAS exome AF: 0.228

Gnomad4 FIN exome AF: 0.168

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.223

GnomAD4 genome AF: 0.203 AC: 30890 AN: 152064 Hom.: 3380 Cov.: 31 AF XY: 0.201 AC XY: 14947 AN XY: 74344

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.205

Alfa AF: 0.221 Hom.: 626

Bravo AF: 0.207

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.48

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: rs1719134; hg19: chr17-34416946;