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GeneBe

rs333

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 4P and 8B. PVS1_StrongBA1

The NM_001394783(CCR5):c.554_585del(p.Ser185IlefsTer32) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152034 control chromosomes in the gnomAD Genomes database, including 553 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.072 ( 553 hom., cov: 31)
Exomes 𝑓: 0.074 ( 966 hom. )

Consequence

CCR5
NM_001394783 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:3O:2

Conservation

PhyloP100: 0.894

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Fraction of 0.48 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCR5NM_001394783.1 linkuse as main transcriptc.554_585del p.Ser185IlefsTer32 frameshift_variant 2/2 ENST00000292303.5
CCR5ASNR_125406.1 linkuse as main transcriptn.392-2067_392-2036del intron_variant, non_coding_transcript_variant
CCR5NM_000579.4 linkuse as main transcriptc.554_585del p.Ser185IlefsTer32 frameshift_variant 3/3
CCR5NM_001100168.2 linkuse as main transcriptc.554_585del p.Ser185IlefsTer32 frameshift_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCR5ENST00000292303.5 linkuse as main transcriptc.554_585del p.Ser185IlefsTer32 frameshift_variant 2/21 NM_001394783.1 P1
CCR5ASENST00000701879.1 linkuse as main transcriptn.174-2067_174-2036del intron_variant, non_coding_transcript_variant
CCR5ENST00000445772.1 linkuse as main transcriptc.554_585del p.Ser185IlefsTer32 frameshift_variant 1/1 P1
CCR5ASENST00000451485.2 linkuse as main transcriptn.392-2067_392-2036del intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0718
AC:
10911
AN:
152034
Hom.:
553
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0204
Gnomad AMI
AF:
0.180
Gnomad AMR
AF:
0.0370
Gnomad ASJ
AF:
0.130
Gnomad EAS
AF:
0.000578
Gnomad SAS
AF:
0.0135
Gnomad FIN
AF:
0.135
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.0483
GnomAD3 exomes
AF:
0.0743
AC:
18640
AN:
251006
Hom.:
966
AF XY:
0.0745
AC XY:
10108
AN XY:
135678
show subpopulations
Gnomad AFR exome
AF:
0.0192
Gnomad AMR exome
AF:
0.0293
Gnomad ASJ exome
AF:
0.129
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0160
Gnomad FIN exome
AF:
0.134
Gnomad NFE exome
AF:
0.108
Gnomad OTH exome
AF:
0.0726
GnomAD4 exome
AF:
0.100
AC:
146811
AN:
1461718
Hom.:
8315
AF XY:
0.0983
AC XY:
71450
AN XY:
727168
show subpopulations
Gnomad4 AFR exome
AF:
0.0154
Gnomad4 AMR exome
AF:
0.0303
Gnomad4 ASJ exome
AF:
0.131
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0171
Gnomad4 FIN exome
AF:
0.131
Gnomad4 NFE exome
AF:
0.115
Gnomad4 OTH exome
AF:
0.0877
Alfa
AF:
0.0929
Hom.:
121
Asia WGS
AF:
0.0120
AC:
43
AN:
3478
EpiCase
AF:
0.0915
EpiControl
AF:
0.0970

ClinVar

Significance: Benign
Submissions summary: Benign:3Other:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 22, 2019- -
Susceptibility to HIV infection Benign:1
protective, no assertion criteria providedliterature onlyOMIMDec 01, 2008- -
Resistance to hepatitis C virus Benign:1
protective, no assertion criteria providedliterature onlyOMIMDec 01, 2008- -
West Nile virus, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMDec 01, 2008- -
Multiple sclerosis modifier of disease progression Other:1
risk factor, no assertion criteria providedliterature onlyOMIMDec 01, 2008- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs333; hg19: chr3-46414943;