ENST00000630386.2:n.101-17261C>T

Variant names:

• chr8-128938144-G-A
• rs1372449
• ENST00000630386.2:n.101-17261C>T

Variant summary

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

The ENST00000630386.2(CCDC26):​n.101-17261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,904 control chromosomes in the GnomAD database, including 8,141 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 (8141 hom., cov: 32)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 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.101-17261C>T		intron_variant	Intron 2 of 6	5
CCDC26	ENST00000643616.1	n.136+26386C>T		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-32976C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48049 AN: 151786 Hom.: 8141 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.316 AC: 48074 AN: 151904 Hom.: 8141 Cov.: 32 AF XY: 0.311 AC XY: 23065 AN XY: 74230

African (AFR) AF: 0.258 AC: 10685 AN: 41474

American (AMR) AF: 0.268 AC: 4085 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1301 AN: 3462

East Asian (EAS) AF: 0.0439 AC: 227 AN: 5168

South Asian (SAS) AF: 0.280 AC: 1353 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3006 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 148 AN: 290

European-Non Finnish (NFE) AF: 0.386 AC: 26182 AN: 67864

Other (OTH) AF: 0.333 AC: 703 AN: 2114

Alfa AF: 0.228 Hom.: 541

Bravo AF: 0.313

Asia WGS AF: 0.178 AC: 621 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	0.58
DANN	Benign	0.78
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1372449; hg19: chr8-129950390;