Variant rs55705857 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_130917.1(CCDC26):n.312+46482T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.038 in 152,314 control chromosomes in the GnomAD database, including 172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.038 ( 172 hom., cov: 32)

Consequence

CCDC26
NR_130917.1 intron, non_coding_transcript

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: 4.18

Variant links:

Genes affected

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

CCDC26 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1 linkuse as main transcript	n.312+46482T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CCDC26	ENST00000446592.7 linkuse as main transcript	n.312+46482T>C	intron_variant, non_coding_transcript_variant	1
CCDC26	ENST00000642958.2 linkuse as main transcript	n.474-5356T>C	intron_variant, non_coding_transcript_variant
CCDC26	ENST00000645432.1 linkuse as main transcript	n.364-46424T>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0380

AC:

5789

AN:

152196

Hom.:

172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00970

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0194

Gnomad ASJ

AF:

0.0147

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0230

Gnomad FIN

AF:

0.0946

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0562

Gnomad OTH

AF:

0.0359

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

GnomAD4 genome

AF:

0.0380

AC:

5789

AN:

152314

Hom.:

172

Cov.:

AF XY:

0.0383

AC XY:

2853

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00967

Gnomad4 AMR

AF:

0.0193

Gnomad4 ASJ

AF:

0.0147

Gnomad4 EAS

AF:

0.000773

Gnomad4 SAS

AF:

0.0230

Gnomad4 FIN

AF:

0.0946

Gnomad4 NFE

AF:

0.0562

Gnomad4 OTH

AF:

0.0355

Alfa

AF:

0.0485

Hom.:

Bravo

AF:

0.0304

Asia WGS

AF:

0.00838

AC:

AN:

3476

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Glioma susceptibility 7

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Oct 20, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.51

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over