Genetic Variant ENST00000643616.1:n.137-74606G>C (chr8-128882775-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000643616.1(CCDC26):n.137-74606G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,040 control chromosomes in the GnomAD database, including 31,801 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 0.64 ( 31801 hom., cov: 33)

Consequence

CCDC26
ENST00000643616.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0970

Publications

1 publications found

Variant links:

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

CCDC26 links:

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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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 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	ENST00000643616.1 link	n.137-74606G>C	intron_variant	Intron 2 of 3
CCDC26	ENST00000675388.1 link	n.654-66081G>C	intron_variant	Intron 6 of 8
CCDC26	ENST00000676248.1 link	n.101-68237G>C	intron_variant	Intron 1 of 4
CCDC26	ENST00000676407.1 link	n.493-54681G>C	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97520

AN:

151922

Hom.:

31768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.601

Gnomad AMI

AF:

0.601

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.942

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.569

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.644

Gnomad OTH

AF:

0.625

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

GnomAD4 genome

AF:

0.642

AC:

97605

AN:

152040

Hom.:

31801

Cov.:

AF XY:

0.643

AC XY:

47766

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.601

AC:

24903

AN:

41462

American (AMR)

AF:

0.717

AC:

10964

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.556

AC:

1929

AN:

3470

East Asian (EAS)

AF:

0.942

AC:

4869

AN:

5168

South Asian (SAS)

AF:

0.643

AC:

3099

AN:

4822

European-Finnish (FIN)

AF:

0.569

AC:

5995

AN:

10542

Middle Eastern (MID)

AF:

0.660

AC:

194

AN:

294

European-Non Finnish (NFE)

AF:

0.644

AC:

43776

AN:

67968

Other (OTH)

AF:

0.628

AC:

1329

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1802

3604

5407

7209

9011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.636

Hom.:

3868

Bravo

AF:

0.655

Asia WGS

AF:

0.762

AC:

2652

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.5

(source)

DANN

Benign

0.72

PhyloP100

0.097

Splicing

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

Publications

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ENST00000643616.1:n.137-74606G>C

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