Genetic Variant ENST00000446592.7:n.312+45071T>A (chr8-129634857-A-T) – 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+45071T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,964 control chromosomes in the GnomAD database, including 14,688 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 0.44 ( 14688 hom., cov: 32)

Consequence

CCDC26
ENST00000446592.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

Publications

1 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1 link	n.312+45071T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCDC26	ENST00000446592.7 link	n.312+45071T>A	intron_variant	Intron 1 of 3	1
CCDC26	ENST00000642958.2 link	n.474-6767T>A	intron_variant	Intron 3 of 3
CCDC26	ENST00000645432.1 link	n.363+45071T>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

66234

AN:

151846

Hom.:

14658

Cov.:

show subpopulations

Gnomad AFR

AF:

0.510

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.405

Gnomad OTH

AF:

0.428

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

GnomAD4 genome

AF:

0.436

AC:

66313

AN:

151964

Hom.:

14688

Cov.:

AF XY:

0.435

AC XY:

32294

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.510

AC:

21135

AN:

41420

American (AMR)

AF:

0.448

AC:

6840

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1221

AN:

3468

East Asian (EAS)

AF:

0.398

AC:

2051

AN:

5152

South Asian (SAS)

AF:

0.460

AC:

2219

AN:

4822

European-Finnish (FIN)

AF:

0.382

AC:

4035

AN:

10564

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.405

AC:

27555

AN:

67954

Other (OTH)

AF:

0.430

AC:

905

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1936

3872

5807

7743

9679

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.426

Hom.:

1779

Bravo

AF:

0.443

Asia WGS

AF:

0.447

AC:

1557

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.5

(source)

DANN

Benign

0.64

PhyloP100

-0.17

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