8-128832281-C-T

Variant names:

• chr8-128832281-C-T
• rs4733652
• ENST00000643616.1:n.137-24112G>A

Variant summary

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

The ENST00000643616.1(CCDC26):​n.137-24112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,082 control chromosomes in the GnomAD database, including 4,565 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 0.21 (4565 hom., cov: 33)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 4 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=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000643616.1	n.137-24112G>A		intron_variant	Intron 2 of 3
CCDC26	ENST00000675388.1	n.654-15587G>A		intron_variant	Intron 6 of 8
CCDC26	ENST00000676248.1	n.101-17743G>A		intron_variant	Intron 1 of 4
CCDC26	ENST00000676407.1	n.493-4187G>A		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32035 AN: 151964 Hom.: 4549 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.211 AC: 32075 AN: 152082 Hom.: 4565 Cov.: 33 AF XY: 0.218 AC XY: 16209 AN XY: 74360

African (AFR) AF: 0.142 AC: 5893 AN: 41474

American (AMR) AF: 0.361 AC: 5526 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3857 AN: 5172

South Asian (SAS) AF: 0.199 AC: 960 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2377 AN: 10570

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12566 AN: 67970

Other (OTH) AF: 0.197 AC: 417 AN: 2114

Alfa AF: 0.184 Hom.: 383

Bravo AF: 0.223

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	19
DANN	Benign	0.65
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs4733652; hg19: chr8-129844527;