rs1719147
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002984.4(CCL4):c.191+90A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,984 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000010 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
CCL4
NM_002984.4 intron
NM_002984.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0820
Genes affected
CCL4 (HGNC:10630): (C-C motif chemokine ligand 4) The protein encoded by this gene is a mitogen-inducible monokine and is one of the major HIV-suppressive factors produced by CD8+ T-cells. The encoded protein is secreted and has chemokinetic and inflammatory functions. [provided by RefSeq, Dec 2012]
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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=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL4 | NM_002984.4 | c.191+90A>C | intron_variant | ENST00000615863.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL4 | ENST00000615863.2 | c.191+90A>C | intron_variant | 1 | NM_002984.4 | P1 | |||
CCL4 | ENST00000621626.1 | c.77-493A>C | intron_variant | 1 | |||||
CCL4 | ENST00000613947.1 | n.892A>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151984Hom.: 0 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000101 AC: 14AN: 1384300Hom.: 1 Cov.: 22 AF XY: 0.0000189 AC XY: 13AN XY: 689404
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151984Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74234
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at