rs1719134

Variant names:

• chr17-36089600-G-A
• rs1719134
• NM_002983.3:c.74-303C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL3	NM_002983.3	MANE Select	c.74-303C>T		intron	N/A	NP_002974.1
	CCL3	NR_168494.1		n.544C>T		non_coding_transcript_exon	Exon 1 of 2
	CCL3-AS1	NR_186417.1		n.384G>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL3	ENST00000613922.2	TSL:1 MANE Select	c.74-303C>T		intron	N/A	ENSP00000477908.1
	CCL3	ENST00000614051.1	TSL:1	n.570C>T		non_coding_transcript_exon	Exon 1 of 2
	CCL3	ENST00000613928.1	TSL:5	n.535C>T		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.135 AC: 1719 AN: 12728

American (AMR) AF: 0.207 AC: 4359 AN: 21074

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 2773 AN: 14322

East Asian (EAS) AF: 0.322 AC: 9177 AN: 28472

South Asian (SAS) AF: 0.228 AC: 11071 AN: 48552

European-Finnish (FIN) AF: 0.168 AC: 4643 AN: 27672

Middle Eastern (MID) AF: 0.191 AC: 384 AN: 2008

European-Non Finnish (NFE) AF: 0.241 AC: 66000 AN: 274096

Other (OTH) AF: 0.223 AC: 5776 AN: 25872

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

African (AFR) AF: 0.134 AC: 5569 AN: 41474

American (AMR) AF: 0.200 AC: 3062 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3472

East Asian (EAS) AF: 0.344 AC: 1777 AN: 5164

South Asian (SAS) AF: 0.237 AC: 1138 AN: 4808

European-Finnish (FIN) AF: 0.156 AC: 1648 AN: 10582

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16314 AN: 67956

Other (OTH) AF: 0.205 AC: 433 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		0.079
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: rs1719134; hg19: chr17-34416946;