Genetic Variant ENST00000644194.1:n.823-5011A>G (chr8-128996987-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000644194.1(CCDC26):n.823-5011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,280 control chromosomes in the GnomAD database, including 436 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 0.063 ( 436 hom., cov: 32)

Consequence

CCDC26
ENST00000644194.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CCDC26	ENST00000644194.1 link	n.823-5011A>G	intron_variant	Intron 6 of 6
CCDC26	ENST00000644557.1 link	n.411-91819A>G	intron_variant	Intron 3 of 3
CCDC26	ENST00000674766.1 link	n.451+20852A>G	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.0634

AC:

9650

AN:

152162

Hom.:

436

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0157

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0753

Gnomad ASJ

AF:

0.0629

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0573

Gnomad FIN

AF:

0.0456

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.0963

Gnomad OTH

AF:

0.0780

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

GnomAD4 genome

AF:

0.0633

AC:

9645

AN:

152280

Hom.:

436

Cov.:

AF XY:

0.0622

AC XY:

4634

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.0157

AC:

651

AN:

41568

American (AMR)

AF:

0.0750

AC:

1147

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0629

AC:

218

AN:

3466

East Asian (EAS)

AF:

0.00116

AC:

AN:

5192

South Asian (SAS)

AF:

0.0571

AC:

276

AN:

4830

European-Finnish (FIN)

AF:

0.0456

AC:

484

AN:

10614

Middle Eastern (MID)

AF:

0.127

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0963

AC:

6550

AN:

68008

Other (OTH)

AF:

0.0762

AC:

161

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

458

915

1373

1830

2288

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0301

Hom.:

Bravo

AF:

0.0634

Asia WGS

AF:

0.0250

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.48

(source)

DANN

Benign

0.55

PhyloP100

-1.8

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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