rs1045879
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_020311.3(ACKR3):c.796C>T(p.Leu266=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,613,720 control chromosomes in the GnomAD database, including 70,825 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 0.36 ( 12731 hom., cov: 33)
Exomes 𝑓: 0.27 ( 58094 hom. )
Consequence
ACKR3
NM_020311.3 synonymous
NM_020311.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.859
Genes affected
ACKR3 (HGNC:23692): (atypical chemokine receptor 3) This gene encodes a member of the G-protein coupled receptor family. Although this protein was earlier thought to be a receptor for vasoactive intestinal peptide (VIP), it is now considered to be an orphan receptor, in that its endogenous ligand has not been identified. The protein is also a coreceptor for human immunodeficiency viruses (HIV). Translocations involving this gene and HMGA2 on chromosome 12 have been observed in lipomas. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
?
Synonymous conserved (PhyloP=0.859 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACKR3 | NM_020311.3 | c.796C>T | p.Leu266= | synonymous_variant | 2/2 | ENST00000272928.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACKR3 | ENST00000272928.4 | c.796C>T | p.Leu266= | synonymous_variant | 2/2 | 2 | NM_020311.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.356 AC: 54152AN: 151986Hom.: 12693 Cov.: 33
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GnomAD3 exomes AF: 0.255 AC: 64055AN: 251410Hom.: 10518 AF XY: 0.257 AC XY: 34962AN XY: 135882
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GnomAD4 exome AF: 0.268 AC: 391137AN: 1461616Hom.: 58094 Cov.: 35 AF XY: 0.269 AC XY: 195894AN XY: 727088
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GnomAD4 genome ? AF: 0.357 AC: 54234AN: 152104Hom.: 12731 Cov.: 33 AF XY: 0.346 AC XY: 25741AN XY: 74376
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at