rs987525

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000630386.2(CCDC26):​n.101-13025G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,970 control chromosomes in the GnomAD database, including 9,264 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 0.30 (9264 hom., cov: 31)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000630386.2	n.101-13025G>T		intron_variant	Intron 2 of 6	5
CCDC26	ENST00000643616.1	n.136+30622G>T		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-28740G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46137 AN: 151852 Hom.: 9237 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.304 AC: 46208 AN: 151970 Hom.: 9264 Cov.: 31 AF XY: 0.296 AC XY: 21998 AN XY: 74262

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.283

Alfa AF: 0.228 Hom.: 9743

Bravo AF: 0.324

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987525; hg19: chr8-129946154;