17-36088230-A-G

Variant summary

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

The ENST00000620056.4(CCL3-AS1):n.390-1316A>G variant causes a intron, non coding transcript 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 ENST00000620056.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCL3	NM_002983.3			downstream_gene_variant		ENST00000613922.2
CCL3	NR_168494.1			downstream_gene_variant
CCL3	NR_168495.1			downstream_gene_variant
CCL3	NR_168496.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL3-AS1	ENST00000620056.4	n.390-1316A>G		intron_variant, non_coding_transcript_variant		5
CCL3-AS1	ENST00000615750.1	n.77-1316A>G		intron_variant, non_coding_transcript_variant		3
CCL3	ENST00000613922.2			downstream_gene_variant		1	NM_002983.3	P1
CCL3	ENST00000614051.1			downstream_gene_variant		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

Gnomad4 AFR exome AF: 0.0465

Gnomad4 AMR exome AF: 0.00883

Gnomad4 ASJ exome AF: 0.00397

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000271

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000539

Gnomad4 OTH exome AF: 0.00346

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0143

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000623

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.00107

Gnomad4 OTH AF: 0.0289

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1719127; hg19: chr17-34415576;