chr8-128992422-C-T

Variant names:

• chr8-128992422-C-T
• rs766811
• ENST00000644194.1:n.823-446G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644194.1(CCDC26):​n.823-446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,084 control chromosomes in the GnomAD database, including 35,002 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 0.68 (35002 hom., cov: 32)
• Consequence: CCDC26 ENST00000644194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644194.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000644194.1		n.823-446G>A		intron	N/A
	CCDC26	ENST00000644557.1		n.411-87254G>A		intron	N/A
	CCDC26	ENST00000674766.1		n.451+25417G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102735 AN: 151966 Hom.: 34987 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.676 AC: 102769 AN: 152084 Hom.: 35002 Cov.: 32 AF XY: 0.675 AC XY: 50205 AN XY: 74342

African (AFR) AF: 0.634 AC: 26294 AN: 41486

American (AMR) AF: 0.649 AC: 9922 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2078 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3479 AN: 5146

South Asian (SAS) AF: 0.500 AC: 2403 AN: 4806

European-Finnish (FIN) AF: 0.799 AC: 8455 AN: 10580

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.706 AC: 47989 AN: 67994

Other (OTH) AF: 0.654 AC: 1384 AN: 2116

Alfa AF: 0.690 Hom.: 4497

Bravo AF: 0.666

Asia WGS AF: 0.532 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.25
PhyloP100		0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs766811;

hg19: chr8-130004668;