Variant 3-46408373-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003965.5(CCRL2):c.294G>T(p.Gly98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,613,968 control chromosomes in the GnomAD database, including 20,229 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 0.19 ( 3394 hom., cov: 33)

Exomes 𝑓: 0.14 ( 16835 hom. )

Consequence

CCRL2
NM_003965.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Variant links:

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]

CCRL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP7

Synonymous conserved (PhyloP=-1.53 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CCRL2	NM_003965.5 linkuse as main transcript	c.294G>T	p.Gly98=	synonymous_variant	2/2	ENST00000399036.4
CCRL2	NM_001130910.2 linkuse as main transcript	c.330G>T	p.Gly110=	synonymous_variant	2/2
CCRL2	XM_011534208.2 linkuse as main transcript	c.294G>T	p.Gly98=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCRL2	ENST00000399036.4 linkuse as main transcript	c.294G>T	p.Gly98=	synonymous_variant	2/2	1	NM_003965.5	P2	O00421-1

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28254

AN:

152076

Hom.:

3388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.338

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0213

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.140

GnomAD3 exomes

AF:

0.126

AC:

31413

AN:

249448

Hom.:

2808

AF XY:

0.119

AC XY:

16094

AN XY:

135322

show subpopulations

Gnomad AFR exome

AF:

0.343

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.149

Gnomad EAS exome

AF:

0.000278

Gnomad SAS exome

AF:

0.0227

Gnomad FIN exome

AF:

0.155

Gnomad NFE exome

AF:

0.144

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

AF:

0.142

AC:

208013

AN:

1461774

Hom.:

16835

Cov.:

AF XY:

0.138

AC XY:

100233

AN XY:

727182

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.105

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0244

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.186

AC:

28297

AN:

152194

Hom.:

3394

Cov.:

AF XY:

0.180

AC XY:

13377

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.338

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.151

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0218

Gnomad4 FIN

AF:

0.152

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.138

Alfa

AF:

0.150

Hom.:

2071

Bravo

AF:

0.191

Asia WGS

AF:

0.0420

AC:

146

AN:

3478

EpiCase

AF:

0.124

EpiControl

AF:

0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.017

DANN

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

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