chr3-46375821-G-T

Position:

• chr3-46375821-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394783.1(CCR5):​c.*1860G>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 0.496 in 166,310 control chromosomes in the GnomAD database, including 20,743 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 0.50 (19156 hom., cov: 29)
  • Exomes 𝑓: 0.46 (1587 hom.)
• Consequence: CCR5 NM_001394783.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR5	NM_001394783.1	c.*1860G>T		3_prime_UTR_variant	2/2	ENST00000292303.5	NP_001381712.1
CCR5AS	NR_125406.1	n.392-4404C>A		intron_variant, non_coding_transcript_variant
CCR5	NM_000579.4	c.*1860G>T		3_prime_UTR_variant	3/3		NP_000570.1
CCR5	NM_001100168.2	c.*1860G>T		3_prime_UTR_variant	3/3		NP_001093638.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR5	ENST00000292303.5	c.*1860G>T		3_prime_UTR_variant	2/2	1	NM_001394783.1	ENSP00000292303	P1
CCR5AS	ENST00000701879.1	n.174-4404C>A		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.392-4404C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75482 AN: 151300 Hom.: 19135 Cov.: 29

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.463 AC: 6890 AN: 14892 Hom.: 1587 Cov.: 0 AF XY: 0.459 AC XY: 3248 AN XY: 7076

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.463

Gnomad4 NFE exome AF: 0.443

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.499 AC: 75540 AN: 151418 Hom.: 19156 Cov.: 29 AF XY: 0.504 AC XY: 37264 AN XY: 74008

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.500

Alfa AF: 0.425 Hom.: 3081

Bravo AF: 0.501

Asia WGS AF: 0.538 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.35

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: rs746492; hg19: chr3-46417312;