chr2-236581153-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_020311.3(ACKR3):c.688G>A(p.Val230Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00273 in 1,614,116 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 44 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 47 hom. )
Consequence
ACKR3
NM_020311.3 missense
NM_020311.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.121
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0028825104).
BP6
?
Variant 2-236581153-G-A is Benign according to our data. Variant chr2-236581153-G-A is described in ClinVar as [Benign]. Clinvar id is 770516.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0138 (2104/152300) while in subpopulation AFR AF= 0.0476 (1976/41548). AF 95% confidence interval is 0.0458. There are 44 homozygotes in gnomad4. There are 949 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 44 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACKR3 | NM_020311.3 | c.688G>A | p.Val230Ile | missense_variant | 2/2 | ENST00000272928.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACKR3 | ENST00000272928.4 | c.688G>A | p.Val230Ile | missense_variant | 2/2 | 2 | NM_020311.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0138 AC: 2095AN: 152182Hom.: 44 Cov.: 33
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GnomAD3 exomes AF: 0.00399 AC: 1003AN: 251344Hom.: 20 AF XY: 0.00300 AC XY: 407AN XY: 135860
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GnomAD4 exome AF: 0.00158 AC: 2306AN: 1461816Hom.: 47 Cov.: 31 AF XY: 0.00141 AC XY: 1023AN XY: 727192
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GnomAD4 genome ? AF: 0.0138 AC: 2104AN: 152300Hom.: 44 Cov.: 33 AF XY: 0.0127 AC XY: 949AN XY: 74468
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ESP6500AA
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212
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565
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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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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