Variant chr4-73837092-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_002993.4(CXCL6):c.239dupT(p.Val81fs) variant causes a frameshift, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00638 in 1,613,146 control chromosomes in the GnomAD database, including 41 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0051 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 38 hom. )

Consequence

CXCL6
NM_002993.4 frameshift, splice_region

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.21

Variant links:

Genes affected

CXCL6 (HGNC:10643): (C-X-C motif chemokine ligand 6) The protein encoded by this gene is a member CXC chemokine family. The encoded protein is a chemotactic for neutrophil granulocytes and has antibacterial action against gram-negative and gram-positive bacteria. This gene and other members of the CXC chemokine gene family form a gene cluster in a region of chromosome 4q. [provided by RefSeq, Jun 2020]

CXCL6 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 4-73837092-G-GT is Benign according to our data. Variant chr4-73837092-G-GT is described in ClinVar as [Benign]. Clinvar id is 710320.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCL6	NM_002993.4 linkuse as main transcript	c.239dupT	p.Val81fs	frameshift_variant, splice_region_variant	2/4	ENST00000226317.10	NP_002984.1	P80162

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCL6	ENST00000226317.10 linkuse as main transcript	c.239dupT	p.Val81fs	frameshift_variant, splice_region_variant	2/4	1	NM_002993.4	ENSP00000226317.5		P80162
CXCL6	ENST00000515050.1 linkuse as main transcript	c.239dupT	p.Val81fs	frameshift_variant, splice_region_variant	2/3	1		ENSP00000424819.1		D6RF92

Frequencies

GnomAD3 genomes

AF:

0.00506

AC:

770

AN:

152256

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00379

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00725

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00528

AC:

1320

AN:

249888

Hom.:

AF XY:

0.00545

AC XY:

736

AN XY:

135104

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00189

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.00315

Gnomad FIN exome

AF:

0.0107

Gnomad NFE exome

AF:

0.00770

Gnomad OTH exome

AF:

0.00494

GnomAD4 exome

AF:

0.00652

AC:

9517

AN:

1460772

Hom.:

Cov.:

AF XY:

0.00638

AC XY:

4636

AN XY:

726688

show subpopulations

Gnomad4 AFR exome

AF:

0.000897

Gnomad4 AMR exome

AF:

0.00220

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00316

Gnomad4 FIN exome

AF:

0.0108

Gnomad4 NFE exome

AF:

0.00741

Gnomad4 OTH exome

AF:

0.00477

GnomAD4 genome

AF:

0.00505

AC:

770

AN:

152374

Hom.:

Cov.:

AF XY:

0.00458

AC XY:

341

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.00180

Gnomad4 AMR

AF:

0.00379

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.0113

Gnomad4 NFE

AF:

0.00725

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00531

Hom.:

Bravo

AF:

0.00464

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00692

EpiControl

AF:

0.00664

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 02, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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