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rs1799864

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001123396.4(CCR2):c.190G>A(p.Val64Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151958 control chromosomes in the gnomAD Genomes database, including 1285 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

Frequency

Genomes: 𝑓 0.12 ( 1285 hom., cov: 32)
Exomes 𝑓: 0.13 ( 2499 hom. )

Consequence

CCR2
NM_001123396.4 missense

Scores

1
16

Clinical Significance

protective no assertion criteria provided B:1

Conservation

PhyloP100: 1.13

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017913282).
BP6
?
Variant 3-46357717-G-A is Benign according to our data. Variant chr3-46357717-G-A is described in ClinVar as [protective]. Clinvar id is 8267. Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCR2NM_001123396.4 linkuse as main transcriptc.190G>A p.Val64Ile missense_variant 2/2 ENST00000445132.3
CCR2NM_001123041.3 linkuse as main transcriptc.190G>A p.Val64Ile missense_variant 2/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCR2ENST00000445132.3 linkuse as main transcriptc.190G>A p.Val64Ile missense_variant 2/21 NM_001123396.4 P2P41597-2
CCR2ENST00000400888.2 linkuse as main transcriptc.190G>A p.Val64Ile missense_variant 1/21 A2P41597-1
CCR2ENST00000421659.1 linkuse as main transcriptc.190G>A p.Val64Ile missense_variant 3/34
CCR2ENST00000465202.1 linkuse as main transcriptn.315-400G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.121
AC:
18420
AN:
151958
Hom.:
1285
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.156
Gnomad AMI
AF:
0.117
Gnomad AMR
AF:
0.172
Gnomad ASJ
AF:
0.125
Gnomad EAS
AF:
0.212
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.0632
Gnomad MID
AF:
0.156
Gnomad NFE
AF:
0.0900
Gnomad OTH
AF:
0.132
GnomAD3 exomes
AF:
0.127
AC:
31797
AN:
251286
Hom.:
2499
AF XY:
0.121
AC XY:
16401
AN XY:
135828
show subpopulations
Gnomad AFR exome
AF:
0.162
Gnomad AMR exome
AF:
0.229
Gnomad ASJ exome
AF:
0.127
Gnomad EAS exome
AF:
0.204
Gnomad SAS exome
AF:
0.111
Gnomad FIN exome
AF:
0.0661
Gnomad NFE exome
AF:
0.0942
Gnomad OTH exome
AF:
0.113
GnomAD4 exome
AF:
0.0943
AC:
137839
AN:
1461864
Hom.:
7970
AF XY:
0.0946
AC XY:
68798
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.167
Gnomad4 AMR exome
AF:
0.223
Gnomad4 ASJ exome
AF:
0.120
Gnomad4 EAS exome
AF:
0.244
Gnomad4 SAS exome
AF:
0.110
Gnomad4 FIN exome
AF:
0.0710
Gnomad4 NFE exome
AF:
0.0803
Gnomad4 OTH exome
AF:
0.102
Alfa
AF:
0.105
Hom.:
1496
Bravo
AF:
0.132
TwinsUK
AF:
0.0769
AC:
285
ALSPAC
AF:
0.0703
AC:
271
ESP6500AA
AF:
0.158
AC:
495
ESP6500EA
AF:
0.0920
AC:
659
ExAC
AF:
0.126
AC:
15351
Asia WGS
AF:
0.184
AC:
638
AN:
3478
EpiCase
AF:
0.0955
EpiControl
AF:
0.0912

ClinVar

Significance: protective
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Susceptibility to HIV infection Benign:1
protective, no assertion criteria providedliterature onlyOMIMMay 18, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.093
BayesDel_addAF
Benign
-0.55
T
BayesDel_noAF
Benign
-0.41
Cadd
Benign
8.6
Dann
Uncertain
0.98
Eigen
Benign
-0.42
Eigen_PC
Benign
-0.35
FATHMM_MKL
Benign
0.56
D
LIST_S2
Benign
0.69
T;T;T;.
MetaRNN
Benign
0.0018
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.78
N;N;.;N
MutationTaster
Benign
1.0
P;P;P
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-0.48
N;N;N;N
REVEL
Benign
0.030
Sift
Benign
0.33
T;T;T;T
Sift4G
Benign
0.38
T;T;T;T
Polyphen
0.079
.;B;.;B
Vest4
0.080
MPC
0.20
ClinPred
0.0028
T
GERP RS
1.6
Varity_R
0.045
gMVP
0.10

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1799864; hg19: chr3-46399208; COSMIC: COSV52748713;