8-129611859-G-C

Variant names:

• chr8-129611859-G-C
• rs1991866
• ENST00000446592.7:n.312+68069C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446592.7(CCDC26):​n.312+68069C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,052 control chromosomes in the GnomAD database, including 24,333 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 0.56 (24333 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 34 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.312+68069C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+68069C>G		intron_variant	Intron 1 of 3	1
CCDC26	ENST00000645432.1	n.364-24837C>G		intron_variant	Intron 2 of 2
CCDC26	ENST00000663066.2	n.634-24837C>G		intron_variant	Intron 3 of 3
CCDC26	ENST00000835909.1	n.266-24837C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85514 AN: 151934 Hom.: 24310 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.563 AC: 85591 AN: 152052 Hom.: 24333 Cov.: 32 AF XY: 0.566 AC XY: 42051 AN XY: 74280

African (AFR) AF: 0.520 AC: 21554 AN: 41432

American (AMR) AF: 0.580 AC: 8866 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1788 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2401 AN: 5172

South Asian (SAS) AF: 0.667 AC: 3218 AN: 4822

European-Finnish (FIN) AF: 0.602 AC: 6357 AN: 10560

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39516 AN: 67982

Other (OTH) AF: 0.564 AC: 1194 AN: 2116

Alfa AF: 0.462 Hom.: 1325

Bravo AF: 0.558

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1991866; hg19: chr8-130624105;