8-128938598-C-T

Variant names:

• chr8-128938598-C-T
• rs7017252
• ENST00000630386.2:n.101-17715G>A

Variant summary

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

The ENST00000630386.2(CCDC26):​n.101-17715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,730 control chromosomes in the GnomAD database, including 8,348 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 0.32 (8348 hom., cov: 31)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000630386.2	n.101-17715G>A		intron_variant	Intron 2 of 6	5
CCDC26	ENST00000643616.1	n.136+25932G>A		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-33430G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48539 AN: 151612 Hom.: 8348 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.320 AC: 48564 AN: 151730 Hom.: 8348 Cov.: 31 AF XY: 0.314 AC XY: 23273 AN XY: 74124

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0440

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.337

Alfa AF: 0.377 Hom.: 20041

Bravo AF: 0.316

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7017252; hg19: chr8-129950844;