chr8-129465577-C-T

Variant names:

• chr8-129465577-C-T
• rs10464870
• ENST00000446592.7:n.360+15066G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446592.7(CCDC26):​n.360+15066G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,144 control chromosomes in the GnomAD database, including 49,698 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (49698 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 10 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446592.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	NR_130917.1		n.360+15066G>A		intron	N/A
	CCDC26	NR_130918.1		n.138-95200G>A		intron	N/A
	CCDC26	NR_130919.1		n.138-65893G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.360+15066G>A		intron	N/A
	CCDC26	ENST00000523151.6	TSL:1	n.136-95200G>A		intron	N/A
	CCDC26	ENST00000520048.1	TSL:3	n.111-65893G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122466 AN: 152028 Hom.: 49669 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.818

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.805 AC: 122545 AN: 152144 Hom.: 49698 Cov.: 32 AF XY: 0.801 AC XY: 59552 AN XY: 74376

African (AFR) AF: 0.868 AC: 36056 AN: 41530

American (AMR) AF: 0.805 AC: 12293 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3468

East Asian (EAS) AF: 0.829 AC: 4285 AN: 5166

South Asian (SAS) AF: 0.857 AC: 4133 AN: 4822

European-Finnish (FIN) AF: 0.643 AC: 6803 AN: 10586

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53334 AN: 67972

Other (OTH) AF: 0.817 AC: 1728 AN: 2114

Alfa AF: 0.797 Hom.: 141304

Bravo AF: 0.819

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		-0.0080

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10464870; hg19: chr8-130477823;