8-129591111-T-C

Variant names:

• chr8-129591111-T-C
• rs2163951
• ENST00000446592.7:n.312+88817A>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+88817A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 151,918 control chromosomes in the GnomAD database, including 55,484 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 0.85 (55484 hom., cov: 29)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.923 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	NR_130917.1		n.312+88817A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.312+88817A>G		intron	N/A
	CCDC26	ENST00000645432.1		n.364-4089A>G		intron	N/A
	CCDC26	ENST00000663066.2		n.634-4089A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129566 AN: 151800 Hom.: 55426 Cov.: 29

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.854 AC: 129682 AN: 151918 Hom.: 55484 Cov.: 29 AF XY: 0.858 AC XY: 63646 AN XY: 74214

African (AFR) AF: 0.806 AC: 33351 AN: 41390

American (AMR) AF: 0.906 AC: 13845 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3212 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4862 AN: 5142

South Asian (SAS) AF: 0.924 AC: 4426 AN: 4792

European-Finnish (FIN) AF: 0.854 AC: 9009 AN: 10552

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58103 AN: 67988

Other (OTH) AF: 0.858 AC: 1806 AN: 2106

Alfa AF: 0.857 Hom.: 37092

Bravo AF: 0.854

Asia WGS AF: 0.924 AC: 3212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2163951; hg19: chr8-130603357;