17-36088374-T-C

Variant names:

• chr17-36088374-T-C
• rs8951
• ENST00000614051.1:n.1376A>G

Variant summary

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

The ENST00000614051.1(CCL3):​n.1376A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 438,862 control chromosomes in the GnomAD database, including 9,752 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 0.17 (2726 hom., cov: 32)
  • Exomes 𝑓: 0.21 (7026 hom.)
• Consequence: CCL3 ENST00000614051.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 8 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL3	NM_002983.3	c.*298A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000613922.2	NP_002974.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL3	ENST00000613922.2	c.*298A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_002983.3	ENSP00000477908.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26492 AN: 152018 Hom.: 2729 Cov.: 32

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.212 AC: 60870 AN: 286726 Hom.: 7026 Cov.: 0 AF XY: 0.212 AC XY: 32130 AN XY: 151822

African (AFR) AF: 0.0690 AC: 588 AN: 8516

American (AMR) AF: 0.182 AC: 2036 AN: 11160

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 1561 AN: 9142

East Asian (EAS) AF: 0.308 AC: 5285 AN: 17136

South Asian (SAS) AF: 0.200 AC: 6461 AN: 32384

European-Finnish (FIN) AF: 0.160 AC: 2322 AN: 14492

Middle Eastern (MID) AF: 0.159 AC: 206 AN: 1292

European-Non Finnish (NFE) AF: 0.222 AC: 39080 AN: 175970

Other (OTH) AF: 0.200 AC: 3331 AN: 16634

GnomAD4 genome AF: 0.174 AC: 26477 AN: 152136 Hom.: 2726 Cov.: 32 AF XY: 0.171 AC XY: 12735 AN XY: 74380

African (AFR) AF: 0.0704 AC: 2921 AN: 41498

American (AMR) AF: 0.177 AC: 2704 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1718 AN: 5184

South Asian (SAS) AF: 0.210 AC: 1009 AN: 4816

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10582

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15358 AN: 67988

Other (OTH) AF: 0.168 AC: 354 AN: 2104

Alfa AF: 0.198 Hom.: 418

Bravo AF: 0.174

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.30
PhyloP100		-1.6
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: rs8951; hg19: chr17-34415720;