rs1719127

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000620056.4(CCL3-AS1):​n.390-1316A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

CCL3-AS1
ENST00000620056.4 intron, non_coding_transcript

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.159
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCL3NM_002983.3 linkuse as main transcript downstream_gene_variant ENST00000613922.2
CCL3NR_168494.1 linkuse as main transcript downstream_gene_variant
CCL3NR_168495.1 linkuse as main transcript downstream_gene_variant
CCL3NR_168496.1 linkuse as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCL3-AS1ENST00000620056.4 linkuse as main transcriptn.390-1316A>C intron_variant, non_coding_transcript_variant 5
CCL3-AS1ENST00000615750.1 linkuse as main transcriptn.77-1316A>C intron_variant, non_coding_transcript_variant 3
CCL3ENST00000613922.2 linkuse as main transcript downstream_gene_variant 1 NM_002983.3 P1
CCL3ENST00000614051.1 linkuse as main transcript downstream_gene_variant 1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
7.4

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1719127; hg19: chr17-34415576; API