ENST00000446592.7:n.312+27767A>G

Variant names:

• chr8-129652161-T-C
• rs9656979
• ENST00000446592.7:n.312+27767A>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+27767A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,874 control chromosomes in the GnomAD database, including 11,410 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 0.38 (11410 hom., cov: 30)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.312+27767A>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+27767A>G		intron_variant	Intron 1 of 3	1
CCDC26	ENST00000642958.2	n.473+16038A>G		intron_variant	Intron 3 of 3
CCDC26	ENST00000645432.1	n.363+27767A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57116 AN: 151756 Hom.: 11403 Cov.: 30

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.376 AC: 57144 AN: 151874 Hom.: 11410 Cov.: 30 AF XY: 0.383 AC XY: 28453 AN XY: 74212

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.388

Alfa AF: 0.407 Hom.: 10700

Bravo AF: 0.371

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9656979; hg19: chr8-130664407;