8-129446893-G-C

Variant names:

• chr8-129446893-G-C
• rs1030626
• ENST00000446592.7:n.360+33750C>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.360+33750C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,986 control chromosomes in the GnomAD database, including 24,678 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 0.57 (24678 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 4 publications found

Genes affected

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

ENSG00000253926 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+33750C>G		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.138-76516C>G		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.138-47209C>G		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.138-47209C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.360+33750C>G		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.136-76516C>G		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.111-47209C>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86196 AN: 151870 Hom.: 24673 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86232 AN: 151986 Hom.: 24678 Cov.: 32 AF XY: 0.565 AC XY: 41974 AN XY: 74268

African (AFR) AF: 0.558 AC: 23150 AN: 41462

American (AMR) AF: 0.647 AC: 9874 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3668 AN: 5154

South Asian (SAS) AF: 0.559 AC: 2694 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4639 AN: 10524

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38098 AN: 67980

Other (OTH) AF: 0.589 AC: 1243 AN: 2112

Alfa AF: 0.423 Hom.: 1087

Bravo AF: 0.582

Asia WGS AF: 0.631 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1030626; hg19: chr8-130459139;