rs55705857

Variant names:

• chr8-129633446-A-G
• rs55705857
• ENST00000446592.7:n.312+46482T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000446592.7(CCDC26):​n.312+46482T>C variant causes a intron 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 ENST00000446592.7 intron
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 4.18
• Publications: 63 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.312+46482T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+46482T>C		intron_variant	Intron 1 of 3	1
CCDC26	ENST00000642958.2	n.474-5356T>C		intron_variant	Intron 3 of 3
CCDC26	ENST00000645432.1	n.364-46424T>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.00967 AC: 402 AN: 41586

American (AMR) AF: 0.0193 AC: 296 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4828

European-Finnish (FIN) AF: 0.0946 AC: 1003 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3822 AN: 68022

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0434 Hom.: 90

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

Oct 20, 2022

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Benign	0.51
PhyloP100		4.2
Mutation Taster		=89/11	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs55705857; hg19: chr8-130645692;