3-46374725-C-T

Variant names:

• chr3-46374725-C-T
• rs17765882
• NM_001394783.1:c.*764C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394783.1(CCR5):​c.*764C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 167,226 control chromosomes in the GnomAD database, including 712 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.067 (527 hom., cov: 32)
  • Exomes 𝑓: 0.16 (185 hom.)
• Consequence: CCR5 NM_001394783.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 11 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR5	NM_001394783.1	c.*764C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000292303.5	NP_001381712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR5	ENST00000292303.5	c.*764C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001394783.1	ENSP00000292303.4

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10278 AN: 152058 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0332

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0593

GnomAD4 exome AF: 0.156 AC: 2349 AN: 15050 Hom.: 185 Cov.: 0 AF XY: 0.155 AC XY: 1110 AN XY: 7184

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.157 AC: 2318 AN: 14732

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.0761 AC: 14 AN: 184

Other (OTH) AF: 0.163 AC: 17 AN: 104

GnomAD4 genome AF: 0.0675 AC: 10270 AN: 152176 Hom.: 527 Cov.: 32 AF XY: 0.0728 AC XY: 5413 AN XY: 74398

African (AFR) AF: 0.0150 AC: 622 AN: 41540

American (AMR) AF: 0.0385 AC: 589 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3470

East Asian (EAS) AF: 0.0333 AC: 172 AN: 5164

South Asian (SAS) AF: 0.194 AC: 936 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1641 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5829 AN: 67994

Other (OTH) AF: 0.0582 AC: 123 AN: 2114

Alfa AF: 0.0626 Hom.: 145

Bravo AF: 0.0531

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		-0.025
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17765882; hg19: chr3-46416216;