Genetic Variant CCR5:c.-11-344_-11-342dupCAA (chr3-46372528-C-CACA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_001394783.1(CCR5):c.-11-344_-11-342dupCAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00609 in 168,008 control chromosomes in the GnomAD database, including 12 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0067 ( 12 hom., cov: 0)

Exomes 𝑓: 0.00043 ( 0 hom. )

Consequence

CCR5
NM_001394783.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Variant links:

Genes affected

CCR5 (HGNC:1606): (C-C motif chemokine receptor 5) This gene encodes a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. This protein is expressed by T cells and macrophages, and is known to be an important co-receptor for macrophage-tropic virus, including HIV, to enter host cells. Defective alleles of this gene have been associated with the HIV infection resistance. The ligands of this receptor include monocyte chemoattractant protein 2 (MCP-2), macrophage inflammatory protein 1 alpha (MIP-1 alpha), macrophage inflammatory protein 1 beta (MIP-1 beta) and regulated on activation normal T expressed and secreted protein (RANTES). Expression of this gene was also detected in a promyeloblastic cell line, suggesting that this protein may play a role in granulocyte lineage proliferation and differentiation. This gene is located at the chemokine receptor gene cluster region. An allelic polymorphism in this gene results in both functional and non-functional alleles; the reference genome represents the functional allele. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2015]

CCR5 links:

CCR5AS (HGNC:54398): (CCR5 antisense RNA)

CCR5AS links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00671 (1017/151540) while in subpopulation AFR AF = 0.0233 (964/41386). AF 95% confidence interval is 0.0221. There are 12 homozygotes in GnomAd4. There are 468 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position FAILED quality control check.

BS2

High AC in GnomAd4 at 1017 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR5	NM_001394783.1 link	c.-11-344_-11-342dupCAA		intron_variant	Intron 1 of 1	ENST00000292303.5	NP_001381712.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCR5	ENST00000292303.5 link	c.-11-364_-11-363insACA	intron_variant	Intron 1 of 1	1	NM_001394783.1	ENSP00000292303.4	P51681
CCR5AS	ENST00000451485.2 link	n.392-1112_392-1111insTGT	intron_variant	Intron 2 of 3	3
CCR5AS	ENST00000701879.1 link	n.174-1112_174-1111insTGT	intron_variant	Intron 1 of 2
CCR5	ENST00000445772.1 link	c.-375_-374insACA	upstream_gene_variant		6		ENSP00000404881.1	P51681

Frequencies

GnomAD3 genomes

AF:

0.00672

AC:

1017

AN:

151422

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0234

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00197

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.00386

GnomAD4 exome

AF:

0.000425

AC:

AN:

16468

Hom.:

AF XY:

0.000524

AC XY:

AN XY:

9542

show subpopulations

Gnomad4 AFR exome

AF:

0.0112

AC:

AN:

268

Gnomad4 AMR exome

AF:

0.00

AC:

AN:

1808

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

234

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

530

Gnomad4 SAS exome

AF:

0.00

AC:

AN:

1350

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

446

Gnomad4 NFE exome

AF:

0.000180

AC:

AN:

11100

Gnomad4 Remaining exome

AF:

0.00287

AC:

AN:

698

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00671

AC:

1017

AN:

151540

Hom.:

Cov.:

AF XY:

0.00632

AC XY:

468

AN XY:

74018

show subpopulations

Gnomad4 AFR

AF:

0.0233

AC:

0.0232929

AN:

0.0232929

Gnomad4 AMR

AF:

0.00197

AC:

0.00196644

AN:

0.00196644

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00

AC:

AN:

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000221

AC:

0.000221219

AN:

0.000221219

Gnomad4 OTH

AF:

0.00382

AC:

0.00382409

AN:

0.00382409

Heterozygous variant carriers

140

187

234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000179

Hom.:

170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism

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.

3-46372528-CACAACAACA-CACAACAACAACA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over