Genetic Variant CCDC26:n.312+6717A>G (chr8-129673211-T-C) – 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 NR_130917.1(CCDC26):n.312+6717A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: NR_130917.1 is not a MANE Select or MANE Plus Clinical transcript for CCDC26; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CCDC26
NR_130917.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

Publications

74 publications found

Variant links:

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA) Implicated in brain cancer and high grade glioma. [provided by Alliance of Genome Resources, Jul 2025]

CCDC26 links:

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new If you want to explore the variant's impact on the transcript NR_130917.1, 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: NR_130917.1. 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
	CCDC26 NR_130917.1		n.312+6717A>G	intron	Intron 1 of 3	Prot:

CCDC26 NR_130917.1

HGVSc / HGVSpn.312+6717A>G

Exon rankIntron 1 of 3

intron

Prot:

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
CCDC26 ENST00000446592.7	TSL:1	n.312+6717A>G	intron	Intron 1 of 3	Prot:
CCDC26 ENST00000642958.2		n.374-4913A>G	intron	Intron 2 of 3	Prot:
CCDC26 ENST00000645432.1		n.363+6717A>G	intron	Intron 2 of 2	Prot:

CCDC26 ENST00000446592.7

TSL:1

HGVSc / HGVSpn.312+6717A>G

Exon rankIntron 1 of 3

intron

Prot:

CCDC26 ENST00000642958.2

HGVSc / HGVSpn.374-4913A>G

Exon rankIntron 2 of 3

intron

Prot:

CCDC26 ENST00000645432.1

HGVSc / HGVSpn.363+6717A>G

Exon rankIntron 2 of 2

intron

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 4 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32
TOPMed (Bravo)	AF: 0.00000756	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00	AC:0	Hom:9913	AN:640248	Cov:

Showing 4 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	0.11
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.072
DANN	Benign	0.48
GPN-Star LLR	N/A	-1.1
GPN-Star score	N/A	1.1
PhyloP100	Benign	-2.1

Showing 7 of 7 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