GeneBe

rs10505543

Positions:

Variant summary

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

The ENST00000446592.7(CCDC26):​n.313-56097C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,266 control chromosomes in the GnomAD database, including 471 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 0.043 ( 471 hom., cov: 33)

Consequence

CCDC26
ENST00000446592.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272
Variant links:
Genes affected
CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

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=-0.68).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC26NR_130917.1 linkn.313-56097C>T intron_variant
CCDC26NR_130918.1 linkn.137+38095C>T intron_variant
CCDC26NR_130919.1 linkn.137+38095C>T intron_variant
CCDC26NR_130920.1 linkn.137+38095C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC26ENST00000446592.7 linkn.313-56097C>T intron_variant 1
CCDC26ENST00000523151.6 linkn.135+38095C>T intron_variant 1
CCDC26ENST00000520048.1 linkn.110+38095C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0429
AC:
6523
AN:
152148
Hom.:
468
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0153
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.0316
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0429
AC:
6539
AN:
152266
Hom.:
471
Cov.:
33
AF XY:
0.0416
AC XY:
3094
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.150
Gnomad4 AMR
AF:
0.0153
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.0313
Alfa
AF:
0.0307
Hom.:
35
Bravo
AF:
0.0489
Asia WGS
AF:
0.00693
AC:
24
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
14
DANN
Benign
0.72

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.

Other links and lift over

dbSNP: rs10505543; hg19: chr8-130549033; API