dbSNP rs5018943: CCDC26:n.293+58184T>C (chr8-129341347-A-G) – 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.293+58184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,040 control chromosomes in the GnomAD database, including 22,930 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 ( 22930 hom., cov: 33)

Consequence

CCDC26
ENST00000644194.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.620

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=-0.51).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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.293+58184T>C	intron_variant	Intron 2 of 6
CCDC26	ENST00000644557.1 link	n.310+58167T>C	intron_variant	Intron 2 of 3
CCDC26	ENST00000646877.1 link	n.183-117978T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

82454

AN:

151922

Hom.:

22879

Cov.:

show subpopulations

Gnomad AFR

AF:

0.638

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.607

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.509

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

GnomAD4 genome

AF:

0.543

AC:

82563

AN:

152040

Hom.:

22930

Cov.:

AF XY:

0.543

AC XY:

40352

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.639

AC:

26493

AN:

41480

American (AMR)

AF:

0.608

AC:

9287

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1661

AN:

3470

East Asian (EAS)

AF:

0.754

AC:

3902

AN:

5178

South Asian (SAS)

AF:

0.524

AC:

2529

AN:

4822

European-Finnish (FIN)

AF:

0.468

AC:

4936

AN:

10546

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.474

AC:

32178

AN:

67954

Other (OTH)

AF:

0.509

AC:

1070

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1912

3824

5737

7649

9561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.506

Hom.:

38852

Bravo

AF:

0.558

Asia WGS

AF:

0.625

AC:

2171

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

0.62

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