rs55705857

chr8-129633446-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_130917.1(CCDC26):n.312+46482T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.038 in 152,314 control chromosomes in the GnomAD database, including 172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.038 (172 hom., cov: 32)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 4.18

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC26	NR_130917.1	n.312+46482T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+46482T>C		intron_variant, non_coding_transcript_variant		1
CCDC26	ENST00000642958.2	n.474-5356T>C		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000645432.1	n.364-46424T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0380 AC: 5789 AN: 152196 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.00970

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0380 AC: 5789 AN: 152314 Hom.: 172 Cov.: 32 AF XY: 0.0383 AC XY: 2853 AN XY: 74478

Gnomad4 AFR AF: 0.00967

Gnomad4 AMR AF: 0.0193

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0946

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0485 Hom.: 46

Bravo AF: 0.0304

Asia WGS AF: 0.00838 AC: 30 AN: 3476

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Glioma susceptibility 7 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Oct 20, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	19
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55705857; hg19: chr8-130645692;