rs987525

Variant names:

• chr8-128933908-C-A
• rs987525
• ENST00000630386.2:n.101-13025G>T

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The ENST00000643616.1(CCDC26):n.136+30622G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000643616.1 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 allele was found at a cumulative frequency of 0.304 (AC=46,208) in the gnomAD database across 151,970 control chromosomes, including 9,264 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.565. 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 0.30 (9264 hom., cov: 31)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 96 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 ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -4 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.565 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000643616.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	CCDC26 ENST00000630386.2	TSL:5	n.101-13025G>T	intron	Intron 2 of 6	Prot:
	CCDC26 ENST00000643616.1		n.136+30622G>T	intron	Intron 2 of 3	Prot:
	CCDC26 ENST00000644557.1		n.411-28740G>T	intron	Intron 3 of 3	Prot:

CCDC26 ENST00000630386.2

TSL:5

HGVSc / HGVSpn.101-13025G>T

Exon rankIntron 2 of 6

intron

Prot:

CCDC26 ENST00000643616.1

HGVSc / HGVSpn.136+30622G>T

Exon rankIntron 2 of 3

intron

Prot:

CCDC26 ENST00000644557.1

HGVSc / HGVSpn.411-28740G>T

Exon rankIntron 3 of 3

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: 0.304	AC:46137	Hom:9237	AN:151852	Cov:31
GnomAD4 genome	AF: 0.304	AC:46208	Hom:9264	AN:151970	Cov:31
TOPMed (Bravo)	AF: 0.324	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.245	AC:194089	Hom:28109	AN:791966	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.319	AC:747	Hom:121	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.0675	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.217	AC:65	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.156	AC:546	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.0470	AC:340	Hom:	AN:7230	Cov:
Qatari Genome	AF: 0.293	AC:51	Hom:	AN:174	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.0509	AC:6246	Hom:180	AN:122692	Cov:
Turkish Variome	AF: 0.241	AC:373	Hom:51	AN:1546	Cov:
UK10K	AF: 0.213	AC:1613	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.0656	AC:588	Hom:24	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	7.9
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.67
GPN-Star LLR	N/A	4.7
GPN-Star score	N/A	-0.35
PhyloP100	Benign	-0.38

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: rs987525;

hg19: chr8-129946154;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar