chr2-236581095-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_020311.3(ACKR3):c.630C>T(p.Ile210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000397 in 1,614,224 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00022 ( 3 hom. )
Consequence
ACKR3
NM_020311.3 synonymous
NM_020311.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.657
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 2-236581095-C-T is Benign according to our data. Variant chr2-236581095-C-T is described in ClinVar as [Benign]. Clinvar id is 710902.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.657 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACKR3 | NM_020311.3 | c.630C>T | p.Ile210= | synonymous_variant | 2/2 | ENST00000272928.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACKR3 | ENST00000272928.4 | c.630C>T | p.Ile210= | synonymous_variant | 2/2 | 2 | NM_020311.3 | P1 | |
ACKR3 | ENST00000447924.1 | c.630C>T | p.Ile210= | synonymous_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00211 AC: 321AN: 152218Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000665 AC: 167AN: 251196Hom.: 1 AF XY: 0.000479 AC XY: 65AN XY: 135756
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GnomAD4 exome AF: 0.000219 AC: 320AN: 1461888Hom.: 3 Cov.: 31 AF XY: 0.000171 AC XY: 124AN XY: 727246
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GnomAD4 genome AF: 0.00211 AC: 321AN: 152336Hom.: 2 Cov.: 33 AF XY: 0.00200 AC XY: 149AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 19, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at