rs17242358

chr8-128952627-G-A

Variant summary

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

The ENST00000675388.1(CCDC26):n.654-135933C>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 0.135 in 152,120 control chromosomes in the GnomAD database, including 1,701 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 0.14 (1701 hom., cov: 32)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.654-135933C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20608 AN: 152002 Hom.: 1701 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.135 AC: 20602 AN: 152120 Hom.: 1701 Cov.: 32 AF XY: 0.131 AC XY: 9722 AN XY: 74362

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.0724

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.149

Alfa AF: 0.182 Hom.: 2928

Bravo AF: 0.134

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.99
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17242358; hg19: chr8-129964873;