8-129591111-T-C

Position:

• chr8-129591111-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446592.7(CCDC26):​n.312+88817A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 151,918 control chromosomes in the GnomAD database, including 55,484 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 0.85 (55484 hom., cov: 29)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

CCDC26 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.312+88817A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+88817A>G		intron_variant		1
CCDC26	ENST00000645432.1	n.364-4089A>G		intron_variant
CCDC26	ENST00000663066.1	n.170-4089A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129566 AN: 151800 Hom.: 55426 Cov.: 29

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.854 AC: 129682 AN: 151918 Hom.: 55484 Cov.: 29 AF XY: 0.858 AC XY: 63646 AN XY: 74214

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.858

Alfa AF: 0.858 Hom.: 27591

Bravo AF: 0.854

Asia WGS AF: 0.924 AC: 3212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2163951; hg19: chr8-130603357;