8-128938598-C-T

Variant names:

• chr8-128938598-C-T
• rs7017252
• ENST00000630386.2:n.101-17715G>A

Variant summary

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

The ENST00000643616.1(CCDC26):​n.136+25932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,730 control chromosomes in the GnomAD database, including 8,348 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 0.32 (8348 hom., cov: 31)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 13 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 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	ENST00000630386.2	TSL:5	n.101-17715G>A		intron	N/A
	CCDC26	ENST00000643616.1		n.136+25932G>A		intron	N/A
	CCDC26	ENST00000644557.1		n.411-33430G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48539 AN: 151612 Hom.: 8348 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.320 AC: 48564 AN: 151730 Hom.: 8348 Cov.: 31 AF XY: 0.314 AC XY: 23273 AN XY: 74124

African (AFR) AF: 0.260 AC: 10770 AN: 41348

American (AMR) AF: 0.271 AC: 4134 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3466

East Asian (EAS) AF: 0.0440 AC: 227 AN: 5154

South Asian (SAS) AF: 0.281 AC: 1350 AN: 4808

European-Finnish (FIN) AF: 0.286 AC: 3005 AN: 10498

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26524 AN: 67896

Other (OTH) AF: 0.337 AC: 710 AN: 2106

Alfa AF: 0.368 Hom.: 38738

Bravo AF: 0.316

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7017252; hg19: chr8-129950844;