8-128852347-C-T

Variant names:

• chr8-128852347-C-T
• rs17818958
• ENST00000643616.1:n.137-44178G>A

Variant summary

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

The ENST00000643616.1(CCDC26):​n.137-44178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,924 control chromosomes in the GnomAD database, including 10,786 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 0.37 (10786 hom., cov: 31)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643616.1. 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	ENST00000643616.1		n.137-44178G>A		intron	N/A
	CCDC26	ENST00000675388.1		n.654-35653G>A		intron	N/A
	CCDC26	ENST00000676248.1		n.101-37809G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55632 AN: 151806 Hom.: 10781 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.366 AC: 55643 AN: 151924 Hom.: 10786 Cov.: 31 AF XY: 0.360 AC XY: 26689 AN XY: 74234

African (AFR) AF: 0.297 AC: 12297 AN: 41446

American (AMR) AF: 0.303 AC: 4630 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3472

East Asian (EAS) AF: 0.143 AC: 736 AN: 5160

South Asian (SAS) AF: 0.387 AC: 1869 AN: 4828

European-Finnish (FIN) AF: 0.326 AC: 3429 AN: 10520

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29939 AN: 67918

Other (OTH) AF: 0.378 AC: 795 AN: 2102

Alfa AF: 0.280 Hom.: 746

Bravo AF: 0.360

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.55
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs17818958; hg19: chr8-129864593;