chr8-128908034-C-A

Variant names:

• chr8-128908034-C-A
• rs997310
• ENST00000630386.2:n.506-2901G>T

Variant summary

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

The ENST00000630386.2(CCDC26):​n.506-2901G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,712 control chromosomes in the GnomAD database, including 8,975 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 (8975 hom., cov: 32)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630386.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000630386.2	TSL:5	n.506-2901G>T		intron	N/A
	CCDC26	ENST00000643616.1		n.136+56496G>T		intron	N/A
	CCDC26	ENST00000644557.1		n.411-2866G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49108 AN: 151596 Hom.: 8956 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.324 AC: 49162 AN: 151712 Hom.: 8975 Cov.: 32 AF XY: 0.318 AC XY: 23580 AN XY: 74150

African (AFR) AF: 0.490 AC: 20291 AN: 41398

American (AMR) AF: 0.271 AC: 4122 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3470

East Asian (EAS) AF: 0.0697 AC: 360 AN: 5168

South Asian (SAS) AF: 0.237 AC: 1139 AN: 4806

European-Finnish (FIN) AF: 0.175 AC: 1845 AN: 10538

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19203 AN: 67780

Other (OTH) AF: 0.321 AC: 676 AN: 2108

Alfa AF: 0.307 Hom.: 9515

Bravo AF: 0.340

Asia WGS AF: 0.183 AC: 634 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.036
DANN	Benign	0.26
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs997310; hg19: chr8-129920280;