chr8-128996987-T-C

Variant names:

• chr8-128996987-T-C
• rs17821251
• ENST00000644194.1:n.823-5011A>G

Variant summary

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

The ENST00000644194.1(CCDC26):​n.823-5011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,280 control chromosomes in the GnomAD database, including 436 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 0.063 (436 hom., cov: 32)
• Consequence: CCDC26 ENST00000644194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644194.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000644194.1		n.823-5011A>G		intron	N/A
	CCDC26	ENST00000644557.1		n.411-91819A>G		intron	N/A
	CCDC26	ENST00000674766.1		n.451+20852A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9650 AN: 152162 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0633 AC: 9645 AN: 152280 Hom.: 436 Cov.: 32 AF XY: 0.0622 AC XY: 4634 AN XY: 74474

African (AFR) AF: 0.0157 AC: 651 AN: 41568

American (AMR) AF: 0.0750 AC: 1147 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0629 AC: 218 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5192

South Asian (SAS) AF: 0.0571 AC: 276 AN: 4830

European-Finnish (FIN) AF: 0.0456 AC: 484 AN: 10614

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0963 AC: 6550 AN: 68008

Other (OTH) AF: 0.0762 AC: 161 AN: 2112

Alfa AF: 0.0301 Hom.: 24

Bravo AF: 0.0634

Asia WGS AF: 0.0250 AC: 89 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.55
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17821251; hg19: chr8-130009233;