ENST00000446592.7:n.312+6717A>C

Variant names:

• chr8-129673211-T-G
• rs4295627
• ENST00000446592.7:n.312+6717A>C

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The ENST00000446592.7(CCDC26):n.312+6717A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000446592.7 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 allele was found at a cumulative frequency of 0.174 (AC=26,492) in the gnomAD database across 152,204 control chromosomes, including 2,405 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.226. 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: 𝑓 0.17 (2405 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 74 publications found

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]

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Benign. The variant received -12 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.2255 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000446592.7. 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>C	intron	Intron 1 of 3	Prot:

CCDC26 NR_130917.1

HGVSc / HGVSpn.312+6717A>C

Exon rankIntron 1 of 3

intron

Prot:

Ensembl Transcripts

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

CCDC26 ENST00000446592.7

TSL:1

HGVSc / HGVSpn.312+6717A>C

Exon rankIntron 1 of 3

intron

Prot:

CCDC26 ENST00000642958.2

HGVSc / HGVSpn.374-4913A>C

Exon rankIntron 2 of 3

intron

Prot:

CCDC26 ENST00000645432.1

HGVSc / HGVSpn.363+6717A>C

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: 0.174	AC:26448	Hom:2390	AN:152086	Cov:32
GnomAD4 genome	AF: 0.174	AC:26492	Hom:2405	AN:152204	Cov:32
TOPMed (Bravo)	AF: 0.178	AC:46994	Hom:4442	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.173	AC:110495	Hom:9913	AN:640248	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.163	AC:381	Hom:34	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.264	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.200	AC:60	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.185	AC:646	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.255	AC:1846	Hom:	AN:7232	Cov:
Qatari Genome	AF: 0.210	AC:37	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.214	AC:26278	Hom:2898	AN:122750	Cov:
Turkish Variome	AF: 0.152	AC:235	Hom:17	AN:1546	Cov:
UK10K	AF: 0.171	AC:1293	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.259	AC:2319	Hom:320	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.11
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.059
DANN	Benign	0.50
GPN-Star LLR	N/A	-1.6
GPN-Star score	N/A	1.6
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.

Other links and lift over

dbSNP: rs4295627;

hg19: chr8-130685457;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar