rs41442546

chr3-46375578-C-Achr3-46375578-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001394783.1(CCR5):c.*1617C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0255 in 165,984 control chromosomes in the GnomAD database, including 77 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 0.027 (74 hom., cov: 30)
  • Exomes 𝑓: 0.013 (3 hom.)
• Consequence: CCR5 NM_001394783.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0268 (4050/151092) while in subpopulation NFE AF= 0.0423 (2869/67826). AF 95% confidence interval is 0.041. There are 74 homozygotes in gnomad4. There are 1783 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High AC in GnomAd at 4050 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5	NM_001394783.1	c.*1617C>A		3_prime_UTR_variant	2/2	ENST00000292303.5
CCR5AS	NR_125406.1	n.392-4161G>T		intron_variant, non_coding_transcript_variant
CCR5	NM_000579.4	c.*1617C>A		3_prime_UTR_variant	3/3
CCR5	NM_001100168.2	c.*1617C>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5	ENST00000292303.5	c.*1617C>A		3_prime_UTR_variant	2/2	1	NM_001394783.1	P1
CCR5AS	ENST00000701879.1	n.174-4161G>T		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.392-4161G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0268 AC: 4050 AN: 150970 Hom.: 74 Cov.: 30

Gnomad AFR AF: 0.00775

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.0381

GnomAD4 exome AF: 0.0128 AC: 190 AN: 14892 Hom.: 3 Cov.: 0 AF XY: 0.0122 AC XY: 86 AN XY: 7072

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0127

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0333

GnomAD4 genome AF: 0.0268 AC: 4050 AN: 151092 Hom.: 74 Cov.: 30 AF XY: 0.0242 AC XY: 1783 AN XY: 73766

Gnomad4 AFR AF: 0.00773

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0423

Gnomad4 OTH AF: 0.0377

Alfa AF: 0.0203 Hom.: 15

Bravo AF: 0.0279

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	7.7
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs41442546; hg19: chr3-46417069;