chr2-236580655-G-C
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020311.3(ACKR3):āc.190G>Cā(p.Val64Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0005 in 1,614,068 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0027 ( 5 hom., cov: 33)
Exomes š: 0.00027 ( 0 hom. )
Consequence
ACKR3
NM_020311.3 missense
NM_020311.3 missense
Scores
3
14
Clinical Significance
Conservation
PhyloP100: 6.00
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0090276).
BP6
Variant 2-236580655-G-C is Benign according to our data. Variant chr2-236580655-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 709371.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACKR3 | NM_020311.3 | c.190G>C | p.Val64Leu | missense_variant | 2/2 | ENST00000272928.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACKR3 | ENST00000272928.4 | c.190G>C | p.Val64Leu | missense_variant | 2/2 | 2 | NM_020311.3 | P1 | |
ACKR3 | ENST00000447924.1 | c.190G>C | p.Val64Leu | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00269 AC: 409AN: 152164Hom.: 5 Cov.: 33
GnomAD3 genomes
AF:
AC:
409
AN:
152164
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000665 AC: 167AN: 251132Hom.: 1 AF XY: 0.000486 AC XY: 66AN XY: 135756
GnomAD3 exomes
AF:
AC:
167
AN:
251132
Hom.:
AF XY:
AC XY:
66
AN XY:
135756
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000274 AC: 400AN: 1461786Hom.: 0 Cov.: 31 AF XY: 0.000239 AC XY: 174AN XY: 727176
GnomAD4 exome
AF:
AC:
400
AN:
1461786
Hom.:
Cov.:
31
AF XY:
AC XY:
174
AN XY:
727176
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00267 AC: 407AN: 152282Hom.: 5 Cov.: 33 AF XY: 0.00253 AC XY: 188AN XY: 74454
GnomAD4 genome
AF:
AC:
407
AN:
152282
Hom.:
Cov.:
33
AF XY:
AC XY:
188
AN XY:
74454
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
34
ESP6500EA
AF:
AC:
0
ExAC
AF:
AC:
97
Asia WGS
AF:
AC:
6
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.013
.;B
Vest4
0.10
MutPred
Loss of catalytic residue at V64 (P = 0.0201);Loss of catalytic residue at V64 (P = 0.0201);
MVP
MPC
0.50
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at