chr17-36088230-A-G

Variant names:

• chr17-36088230-A-G
• rs1719127
• ENST00000615750.2:n.544-1316A>G

Variant summary

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

The ENST00000615750.2(CCL3-AS1):​n.544-1316A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 178,734 control chromosomes in the GnomAD database, including 259 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 0.033 (259 hom., cov: 32)
  • Exomes 𝑓: 0.0018 (0 hom.)
• Consequence: CCL3-AS1 ENST00000615750.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 2 publications found

Genes affected

CCL3-AS1 (HGNC:55229): (CCL3 antisense RNA 1)

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]

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 (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL3	NM_002983.3	c.*442T>C		downstream_gene_variant		ENST00000613922.2	NP_002974.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL3	ENST00000613922.2	c.*442T>C		downstream_gene_variant		1	NM_002983.3	ENSP00000477908.1

Frequencies

GnomAD3 genomes AF: 0.0333 AC: 5066 AN: 152100 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0143

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00107

Gnomad OTH AF: 0.0292

GnomAD4 exome AF: 0.00177 AC: 47 AN: 26516 Hom.: 0 Cov.: 0 AF XY: 0.00153 AC XY: 21 AN XY: 13726

African (AFR) AF: 0.0465 AC: 8 AN: 172

American (AMR) AF: 0.00883 AC: 21 AN: 2378

Ashkenazi Jewish (ASJ) AF: 0.00397 AC: 2 AN: 504

East Asian (EAS) AF: 0.00 AC: 0 AN: 542

South Asian (SAS) AF: 0.000271 AC: 1 AN: 3690

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 982

Middle Eastern (MID) AF: 0.0104 AC: 1 AN: 96

European-Non Finnish (NFE) AF: 0.000539 AC: 9 AN: 16708

Other (OTH) AF: 0.00346 AC: 5 AN: 1444

GnomAD4 genome AF: 0.0333 AC: 5074 AN: 152218 Hom.: 259 Cov.: 32 AF XY: 0.0318 AC XY: 2365 AN XY: 74426

African (AFR) AF: 0.113 AC: 4703 AN: 41502

American (AMR) AF: 0.0143 AC: 219 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000623 AC: 3 AN: 4818

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10606

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00107 AC: 73 AN: 68018

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0205 Hom.: 26

Bravo AF: 0.0394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
PhyloP100		-0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1719127; hg19: chr17-34415576;