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GeneBe

rs1799987

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_125406.1(CCR5AS):n.565+800T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,794 control chromosomes in the GnomAD database, including 18,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 18573 hom., cov: 30)

Consequence

CCR5AS
NR_125406.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Benign criteria provided, single submitter P:1B:3

Conservation

PhyloP100: -0.587
Variant links:
Genes affected
CCR5AS (HGNC:54398): (CCR5 antisense RNA)

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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 (BayesDel_noAF=-0.9).
BP6
Variant 3-46370444-A-G is Benign according to our data. Variant chr3-46370444-A-G is described in ClinVar as [Benign]. Clinvar id is 8189.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCR5ASNR_125406.1 linkuse as main transcriptn.565+800T>C intron_variant, non_coding_transcript_variant
CCR5NM_000579.4 linkuse as main transcriptc.-301+246A>G intron_variant
CCR5NM_001100168.2 linkuse as main transcriptc.-66+246A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCR5ASENST00000701879.1 linkuse as main transcriptn.347+800T>C intron_variant, non_coding_transcript_variant
CCR5ASENST00000451485.2 linkuse as main transcriptn.565+800T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.491
AC:
74529
AN:
151674
Hom.:
18552
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.571
Gnomad AMI
AF:
0.466
Gnomad AMR
AF:
0.460
Gnomad ASJ
AF:
0.444
Gnomad EAS
AF:
0.589
Gnomad SAS
AF:
0.610
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.570
Gnomad NFE
AF:
0.441
Gnomad OTH
AF:
0.496
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.491
AC:
74586
AN:
151794
Hom.:
18573
Cov.:
30
AF XY:
0.496
AC XY:
36779
AN XY:
74166
show subpopulations
Gnomad4 AFR
AF:
0.571
Gnomad4 AMR
AF:
0.460
Gnomad4 ASJ
AF:
0.444
Gnomad4 EAS
AF:
0.588
Gnomad4 SAS
AF:
0.612
Gnomad4 FIN
AF:
0.460
Gnomad4 NFE
AF:
0.441
Gnomad4 OTH
AF:
0.492
Alfa
AF:
0.458
Hom.:
3595
Bravo
AF:
0.493
Asia WGS
AF:
0.535
AC:
1859
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Pathogenic:1Benign:3
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Acquired immunodeficiency syndrome, delayed progression to Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMMar 01, 2003- -
Susceptibility to HIV infection Benign:1
protective, no assertion criteria providedliterature onlyOMIMJul 08, 2003- -
CCR5 PROMOTER POLYMORPHISM Benign:1
Benign, no assertion criteria providedliterature onlyOMIMJul 08, 2003- -
CCR5-related condition Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesFeb 18, 2021This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.98
Dann
Benign
0.40

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: rs1799987; hg19: chr3-46411935; API