Genetic Variant ENST00000630386.2:n.101-17715G>A (chr8-128938598-C-T) – 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.101-17715G>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
ENST00000630386.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.469

Publications

13 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 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.101-17715G>A	intron_variant	Intron 2 of 6	5
CCDC26	ENST00000643616.1 link	n.136+25932G>A	intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1 link	n.411-33430G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48539

AN:

151612

Hom.:

8348

Cov.:

show subpopulations

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.:

AF XY:

0.314

AC XY:

23273

AN XY:

74124

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1583

3167

4750

6334

7917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.368

Hom.:

38738

Bravo

AF:

0.316

Asia WGS

AF:

0.178

AC:

622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.72

(source)

DANN

Benign

0.41

PhyloP100

-0.47

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