GeneBe

8-129405378-T-G

Position:

Variant summary

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

The ENST00000446592.7(CCDC26):​n.361-35001A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,222 control chromosomes in the GnomAD database, including 2,494 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 0.17 ( 2494 hom., cov: 32)

Consequence

CCDC26
ENST00000446592.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0380
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC26NR_130917.1 linkn.361-35001A>C intron_variant
CCDC26NR_130918.1 linkn.138-35001A>C intron_variant
CCDC26NR_130919.1 linkn.138-5694A>C intron_variant
CCDC26NR_130920.1 linkn.138-5694A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC26ENST00000446592.7 linkn.361-35001A>C intron_variant 1
CCDC26ENST00000523151.6 linkn.136-35001A>C intron_variant 1
CCDC26ENST00000520048.1 linkn.111-5694A>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
26306
AN:
152104
Hom.:
2491
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.211
Gnomad AMI
AF:
0.0559
Gnomad AMR
AF:
0.151
Gnomad ASJ
AF:
0.185
Gnomad EAS
AF:
0.279
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.0984
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.160
Gnomad OTH
AF:
0.187
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.173
AC:
26305
AN:
152222
Hom.:
2494
Cov.:
32
AF XY:
0.168
AC XY:
12519
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.211
Gnomad4 AMR
AF:
0.151
Gnomad4 ASJ
AF:
0.185
Gnomad4 EAS
AF:
0.279
Gnomad4 SAS
AF:
0.154
Gnomad4 FIN
AF:
0.0984
Gnomad4 NFE
AF:
0.160
Gnomad4 OTH
AF:
0.189
Alfa
AF:
0.119
Hom.:
294
Bravo
AF:
0.179
Asia WGS
AF:
0.230
AC:
801
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.6
DANN
Benign
0.59

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: rs2568409; hg19: chr8-130417624; API