rs987525

Variant names:

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

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 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: 91 publications found

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

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 = 0.5647 — exceeds 5%% threshold (BA1 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
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	N/A
	CCDC26	ENST00000643616.1		n.136+30622G>T		intron	N/A
	CCDC26	ENST00000644557.1		n.411-28740G>T		intron	N/A

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

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
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.

Other links and lift over

dbSNP: rs987525;

hg19: chr8-129946154;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar