3-46410189-A-G

Variant names:

• chr3-46410189-A-G
• rs1015164
• ENST00000441909.1:n.167+509A>G

Variant summary

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

The ENST00000441909.1(CCRL2):​n.167+509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,134 control chromosomes in the GnomAD database, including 44,522 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 0.76 (44522 hom., cov: 33)
• Consequence: CCRL2 ENST00000441909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 38 publications found

Genes affected

CCRL2 (HGNC:1612): (C-C motif chemokine receptor like 2) This gene encodes a chemokine receptor like protein, which is predicted to be a seven transmembrane protein and most closely related to CCR1. Chemokines and their receptors mediated signal transduction are critical for the recruitment of effector immune cells to the site of inflammation. This gene is expressed at high levels in primary neutrophils and primary monocytes, and is further upregulated on neutrophil activation and during monocyte to macrophage differentiation. The function of this gene is unknown. This gene is mapped to the region where the chemokine receptor gene cluster is located. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCRL2	ENST00000441909.1	TSL:2	n.167+509A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115230 AN: 152016 Hom.: 44461 Cov.: 33

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.749

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.758 AC: 115337 AN: 152134 Hom.: 44522 Cov.: 33 AF XY: 0.759 AC XY: 56459 AN XY: 74358

African (AFR) AF: 0.904 AC: 37565 AN: 41538

American (AMR) AF: 0.739 AC: 11303 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2659 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4186 AN: 5156

South Asian (SAS) AF: 0.760 AC: 3663 AN: 4818

European-Finnish (FIN) AF: 0.675 AC: 7122 AN: 10558

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46303 AN: 67976

Other (OTH) AF: 0.741 AC: 1568 AN: 2116

Alfa AF: 0.712 Hom.: 67489

Bravo AF: 0.770

Asia WGS AF: 0.752 AC: 2615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.49
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1015164; hg19: chr3-46451680;