Genetic Variant ENST00000446592.7:n.360+2676C>A (chr8-129477967-G-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.360+2676C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,064 control chromosomes in the GnomAD database, including 7,162 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 0.30 ( 7162 hom., cov: 32)

Consequence

CCDC26
ENST00000446592.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.709

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
CCDC26	NR_130917.1 link	n.360+2676C>A	intron_variant	Intron 2 of 3
CCDC26	NR_130918.1 link	n.137+96915C>A	intron_variant	Intron 1 of 2
CCDC26	NR_130919.1 link	n.138-78283C>A	intron_variant	Intron 1 of 3
CCDC26	NR_130920.1 link	n.138-78283C>A	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCDC26	ENST00000446592.7 link	n.360+2676C>A	intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6 link	n.135+96915C>A	intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1 link	n.111-78283C>A	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45384

AN:

151946

Hom.:

7157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.280

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

GnomAD4 genome

AF:

0.299

AC:

45403

AN:

152064

Hom.:

7162

Cov.:

AF XY:

0.299

AC XY:

22254

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.285

AC:

11824

AN:

41478

American (AMR)

AF:

0.280

AC:

4277

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

801

AN:

3464

East Asian (EAS)

AF:

0.131

AC:

679

AN:

5178

South Asian (SAS)

AF:

0.174

AC:

837

AN:

4820

European-Finnish (FIN)

AF:

0.410

AC:

4330

AN:

10552

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.320

AC:

21753

AN:

67980

Other (OTH)

AF:

0.280

AC:

591

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1587

3174

4761

6348

7935

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<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:

0.329

Hom.:

1091

Bravo

AF:

0.290

Asia WGS

AF:

0.154

AC:

534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.8

(source)

DANN

Benign

0.35

PhyloP100

-0.71

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