Variant rs997310 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000630386.2(CCDC26):n.506-2901G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,712 control chromosomes in the GnomAD database, including 8,975 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 0.32 ( 8975 hom., cov: 32)

Consequence

CCDC26
ENST00000630386.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.63

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CCDC26	ENST00000630386.2 link	n.506-2901G>T	intron_variant	5
CCDC26	ENST00000643616.1 link	n.136+56496G>T	intron_variant
CCDC26	ENST00000644557.1 link	n.411-2866G>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49108

AN:

151596

Hom.:

8956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.490

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.0697

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.324

AC:

49162

AN:

151712

Hom.:

8975

Cov.:

AF XY:

0.318

AC XY:

23580

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.490

Gnomad4 AMR

AF:

0.271

Gnomad4 ASJ

AF:

0.317

Gnomad4 EAS

AF:

0.0697

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.321

Alfa

AF:

0.279

Hom.:

3967

Bravo

AF:

0.340

Asia WGS

AF:

0.183

AC:

634

AN:

3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.036

DANN

Benign

0.26

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over