Genetic Variant ENST00000446592.7:n.312+78560C>T (chr8-129601368-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000446592.7(CCDC26):n.312+78560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,858 control chromosomes in the GnomAD database, including 22,463 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 0.54 ( 22463 hom., cov: 31)

Consequence

CCDC26
ENST00000446592.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.863

Publications

11 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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1 link	n.312+78560C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCDC26	ENST00000446592.7 link	n.312+78560C>T	intron_variant	Intron 1 of 3	1
CCDC26	ENST00000645432.1 link	n.364-14346C>T	intron_variant	Intron 2 of 2
CCDC26	ENST00000663066.2 link	n.634-14346C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

81904

AN:

151740

Hom.:

22447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.543

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.662

Gnomad FIN

AF:

0.592

Gnomad MID

AF:

0.643

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.545

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

GnomAD4 genome

AF:

0.540

AC:

81950

AN:

151858

Hom.:

22463

Cov.:

AF XY:

0.542

AC XY:

40272

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.471

AC:

19506

AN:

41388

American (AMR)

AF:

0.549

AC:

8382

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.507

AC:

1757

AN:

3468

East Asian (EAS)

AF:

0.410

AC:

2115

AN:

5164

South Asian (SAS)

AF:

0.662

AC:

3182

AN:

4808

European-Finnish (FIN)

AF:

0.592

AC:

6236

AN:

10534

Middle Eastern (MID)

AF:

0.654

AC:

191

AN:

292

European-Non Finnish (NFE)

AF:

0.573

AC:

38931

AN:

67930

Other (OTH)

AF:

0.550

AC:

1157

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1876

3752

5627

7503

9379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

718

1436

2154

2872

3590

<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:

0.548

Hom.:

35822

Bravo

AF:

0.529

Asia WGS

AF:

0.537

AC:

1862

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.1

(source)

DANN

Benign

0.30

PhyloP100

-0.86

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