rs987525

Positions:

• chr8-128933908-C-A

Variant summary

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

The ENST00000675388.1(CCDC26):​n.654-117214G>T 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 0.304 in 151,970 control chromosomes in the GnomAD database, including 9,264 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 0.30 (9264 hom., cov: 31)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

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 (AFR) allele frequency at 95% confidence interval = 0.565 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.654-117214G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46137 AN: 151852 Hom.: 9237 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.304 AC: 46208 AN: 151970 Hom.: 9264 Cov.: 31 AF XY: 0.296 AC XY: 21998 AN XY: 74262

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.283

Alfa AF: 0.228 Hom.: 9743

Bravo AF: 0.324

Asia WGS AF: 0.156 AC: 546 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	1.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987525; hg19: chr8-129946154;