8-128996987-T-C

Position:

• chr8-128996987-T-C

Variant summary

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

The ENST00000675388.1(CCDC26):​n.653+105303A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,280 control chromosomes in the GnomAD database, including 436 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 0.063 (436 hom., cov: 32)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000675388.1	n.653+105303A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9650 AN: 152162 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0633 AC: 9645 AN: 152280 Hom.: 436 Cov.: 32 AF XY: 0.0622 AC XY: 4634 AN XY: 74474

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0750

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0456

Gnomad4 NFE AF: 0.0963

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0372 Hom.: 21

Bravo AF: 0.0634

Asia WGS AF: 0.0250 AC: 89 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17821251; hg19: chr8-130009233;