17-36104732-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002984.4(CCL4):c.191+90A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 1,535,036 control chromosomes in the GnomAD database, including 453,608 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 0.76 ( 44684 hom., cov: 31)
Exomes 𝑓: 0.77 ( 408924 hom. )
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCL4 | ENST00000615863.2 | c.191+90A>G | intron_variant | Intron 2 of 2 | 1 | NM_002984.4 | ENSP00000482259.1 | |||
CCL4 | ENST00000621626.1 | c.77-493A>G | intron_variant | Intron 1 of 1 | 1 | ENSP00000480569.1 | ||||
CCL4 | ENST00000613947.1 | n.892A>G | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.765 AC: 116182AN: 151944Hom.: 44641 Cov.: 31
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GnomAD4 exome AF: 0.768 AC: 1061573AN: 1382974Hom.: 408924 Cov.: 22 AF XY: 0.765 AC XY: 526869AN XY: 688822
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GnomAD4 genome AF: 0.765 AC: 116282AN: 152062Hom.: 44684 Cov.: 31 AF XY: 0.765 AC XY: 56891AN XY: 74340
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at