Genetic Variant ENST00000630386.2:n.506-2901G>T (chr8-128908034-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.63

Publications

3 publications found

Variant links:

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

CCDC26 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCDC26	ENST00000630386.2 link	n.506-2901G>T	intron_variant	Intron 6 of 6	5
CCDC26	ENST00000643616.1 link	n.136+56496G>T	intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1 link	n.411-2866G>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49108

AN:

151596

Hom.:

8956

Cov.:

show subpopulations

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.:

AF XY:

0.318

AC XY:

23580

AN XY:

74150

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1635

3270

4904

6539

8174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.036

(source)

DANN

Benign

0.26

PhyloP100

-2.6

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over