chr12-8456137-G-A

Variant names:

• chr12-8456137-G-A
• rs1939672947
• NM_001007033.2:c.26G>A
• CLEC6A p.Ser9Asn

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+1 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 1 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB3_Supporting

The NM_001007033.2(CLEC6A):c.26G>A (p.Ser9Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.000000684 (AC=1) in the gnomAD database across 1,461,454 control chromosomes (no homozygotes observed). The grpmax filtering allele frequency (95% CI) is 0.000000899. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. 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.S9T: Uncertain_significance (ClinVar VariationId 3493609, 1 star) The variant has been observed in cBioPortal in 1 sample across 1 study and 1 cancer type; somatic enrichment level: NONE (Observed in at most one deduplicated cBioPortal case.).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CLEC6A NM_001007033.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 0 publications found

Genes affected

CLEC6A (HGNC:14556): (C-type lectin domain containing 6A) The protein encoded by this gene is a type II membrane receptor with an extracellular C-type lectin-like domain fold. The extracellular portion binds structures with a high mannose content and has been shown to recognize several pathogens, including C. elegans, S. cerevisiae, M. tuberculosis, C. neoformans, and house dust mite. When stimulated, the encoded protein initiates signalling through the CARD9-Bcl10-Malt1 pathway, leading to the induction of cytokines. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 1 points.

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 = 0.000001, AC = 1 — absent/extremely rare (O3 moderate [+2])
	B3Computational evidence does not support deleterious effect		Computational evidence does not support a deleterious effect; Missense variant — primary computational scorer does not support an oncogenic/deleterious effect; supports B3

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001007033.2. 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
	CLEC6A NM_001007033.2	MANE Select	c.26G>A p.Ser9Asn	missense	Exon 1 of 6	Prot: NP_001007034.1 UniProt:
	CLEC6A NM_001317999.2		c.26G>A p.Ser9Asn	missense	Exon 1 of 5	Prot: NP_001304928.1 UniProt:

CLEC6A NM_001007033.2

MANE Select

HGVSc / HGVSpc.26G>Ap.Ser9Asn

Exon rankExon 1 of 6

missense

Prot: NP_001007034.1UniProt: Q6EIG7-1

CLEC6A NM_001317999.2

HGVSc / HGVSpc.26G>Ap.Ser9Asn

Exon rankExon 1 of 5

missense

Prot: NP_001304928.1UniProt: Q6EIG7-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	CLEC6A ENST00000382073.4	TSL:1MANE Select	c.26G>A p.Ser9Asn	missense	Exon 1 of 6	Prot: ENSP00000371505.3 UniProt:

CLEC6A ENST00000382073.4

TSL:1MANE Select

HGVSc / HGVSpc.26G>Ap.Ser9Asn

Exon rankExon 1 of 6

missense

Prot: ENSP00000371505.3UniProt: Q6EIG7-1

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 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF: 6.84e-7	AC:1	Hom:0	AN:1461454	Cov:30
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

Case/control cohorts

Cohort	Cases			Controls
	AF	AC	AN	AF	AC	AN
SCHEMA(Schizophrenia)	0.0000206	1	48432	0.00	0	74528

Showing 1 cohortAllele count / allele number. AF is computed from the counts for ASC (not provided by the source).

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	8.2
AlphaMissense	Benign	0.062
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.72
DEOGEN2	Benign	0.025	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.022	N
FuncVEP CTI	Benign	0.029
GPN-Star LLR	N/A	0.023
GPN-Star score	N/A	-0.023
LIST_S2	Benign	0.25	T
M_CAP	Benign	0.00085	T
MetaRNN	Benign	0.047	T
MetaSVM	Benign	-0.99	T
Mutation Taster	N/A	99/1	polymorphism
MutationAssessor	Benign	-0.34	N
PhyloP100	Benign	-0.62
popEVE	Benign	-3.3
PrimateAI	Benign	0.26	T
PromoterAI	N/A	0.021	Neutral
PROVEAN	Benign	-0.29	N
REVEL	Benign	0.027
Sift	Benign	0.42	T
Sift4G	Benign	0.98	T
Varity_R	N/A	0.037
VESM-3B	Benign	-2.9

Showing 29 of 29 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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.

Other links and lift over

dbSNP: rs1939672947;

hg19: chr12-8608733;

COSMIC: COSV65988027;

COSMIC: COSV65988027;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar