Variant 3-46409113-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM4BP6_Very_StrongBS2

The NM_003965.5(CCRL2):c.1034A>C(p.Ter345SerextTer10) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000456 in 1,597,866 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0025 ( 1 hom., cov: 33)

Exomes 𝑓: 0.00024 ( 2 hom. )

Consequence

CCRL2
NM_003965.5 stop_lost

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.219

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

PM4

Stoplost variant in NM_003965.5 Downstream stopcodon found after 429 codons.

BP6

Variant 3-46409113-A-C is Benign according to our data. Variant chr3-46409113-A-C is described in ClinVar as [Benign]. Clinvar id is 711365.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CCRL2	NM_003965.5 linkuse as main transcript	c.1034A>C	p.Ter345SerextTer10	stop_lost	2/2	ENST00000399036.4
CCRL2	NM_001130910.2 linkuse as main transcript	c.1070A>C	p.Ter357SerextTer10	stop_lost	2/2
CCRL2	XM_011534208.2 linkuse as main transcript	c.1034A>C	p.Ter345SerextTer10	stop_lost	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCRL2	ENST00000399036.4 linkuse as main transcript	c.1034A>C	p.Ter345SerextTer10	stop_lost	2/2	1	NM_003965.5	P2	O00421-1
CCRL2	ENST00000357392.4 linkuse as main transcript	c.1070A>C	p.Ter357SerextTer10	stop_lost	2/2	1		A2	O00421-2
CCRL2	ENST00000400880.3 linkuse as main transcript	c.1034A>C	p.Ter345SerextTer?	stop_lost	2/2	1		P2	O00421-1
CCRL2	ENST00000400882.2 linkuse as main transcript	c.1034A>C	p.Ter345SerextTer10	stop_lost	1/1			P2	O00421-1

Frequencies

GnomAD3 genomes

AF:

0.00246

AC:

375

AN:

152248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00883

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.000620

AC:

149

AN:

240346

Hom.:

AF XY:

0.000469

AC XY:

AN XY:

130110

show subpopulations

Gnomad AFR exome

AF:

0.00904

Gnomad AMR exome

AF:

0.000276

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000911

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000244

AC:

352

AN:

1445500

Hom.:

Cov.:

AF XY:

0.000209

AC XY:

150

AN XY:

716820

show subpopulations

Gnomad4 AFR exome

AF:

0.00945

Gnomad4 AMR exome

AF:

0.000350

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000635

Gnomad4 OTH exome

AF:

0.000284

GnomAD4 genome

AF:

0.00247

AC:

377

AN:

152366

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

189

AN XY:

74516

show subpopulations

Gnomad4 AFR

AF:

0.00885

Gnomad4 AMR

AF:

0.000261

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.000413

Hom.:

Bravo

AF:

0.00261

ESP6500AA

AF:

0.00854

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000835

AC:

101

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

DANN

Benign

0.48

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.61

FATHMM_MKL

Benign

0.19

MutationTaster

Benign

1.0

N;N;N;N

Vest4

0.16

GERP RS

-3.5

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over