Genetic Variant CXCL6:p.Val11Ala (chr4-73836782-TC-CG) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NM_002993.4(CXCL6):c.32_33delTCinsCG (p.Val11Ala) variant causes a missense change. The gene CXCL6 is a known oncogene (CancerMine: 1 oncogene citations). Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.V11A: Uncertain_significance (ClinVar VariationId 2252680, 1 star)

Frequency

Genomes: not found (cov: 32)

Consequence

CXCL6
NM_002993.4 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121

Publications

0 publications found

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:

ENSG00000298131 (HGNC:):

ENSG00000298131 links:

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new If you want to explore the variant's impact on the transcript NM_002993.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_002993.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	CXCL6 NM_002993.4	MANE Select	c.32_33delTCinsCG p.Val11Ala	missense	N/A	Prot: NP_002984.1 UniProt: P80162

CXCL6 NM_002993.4

MANE Select

HGVSc / HGVSpc.32_33delTCinsCGp.Val11Ala

Exon rankN/A

missense

Prot: NP_002984.1UniProt: P80162

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
CXCL6 ENST00000226317.10	TSL:1MANE Select	c.32_33delTCinsCG p.Val11Ala	missense	N/A	Prot: ENSP00000226317.5 UniProt: P80162
CXCL6 ENST00000515050.1	TSL:1	c.32_33delTCinsCG p.Val11Ala	missense	N/A	Prot: ENSP00000424819.1 UniProt: D6RF92
ENSG00000298131 ENST00000753200.1		n.195_196delGAinsCG	non_coding_transcript_exon	Exon 1 of 1	Prot:

CXCL6 ENST00000226317.10

TSL:1MANE Select

HGVSc / HGVSpc.32_33delTCinsCGp.Val11Ala

Exon rankN/A

missense

Prot: ENSP00000226317.5UniProt: P80162

CXCL6 ENST00000515050.1

TSL:1

HGVSc / HGVSpc.32_33delTCinsCGp.Val11Ala

Exon rankN/A

missense

Prot: ENSP00000424819.1UniProt: D6RF92

ENSG00000298131 ENST00000753200.1

HGVSc / HGVSpn.195_196delGAinsCG

Exon rankExon 1 of 1

non_coding_transcript_exon

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 2 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Benign	-0.12

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence