rs9297781

Variant names:

• chr8-129017120-A-C
• rs9297781
• ENST00000644194.1:n.822+719T>G

Variant summary

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

The ENST00000644194.1(CCDC26):​n.822+719T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,068 control chromosomes in the GnomAD database, including 30,715 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 0.62 (30715 hom., cov: 32)
• Consequence: CCDC26 ENST00000644194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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.822+719T>G		intron	N/A
	CCDC26	ENST00000644557.1		n.410+85170T>G		intron	N/A
	CCDC26	ENST00000674766.1		n.451+719T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95009 AN: 151950 Hom.: 30706 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.625 AC: 95021 AN: 152068 Hom.: 30715 Cov.: 32 AF XY: 0.625 AC XY: 46485 AN XY: 74348

African (AFR) AF: 0.462 AC: 19160 AN: 41484

American (AMR) AF: 0.623 AC: 9508 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2278 AN: 3468

East Asian (EAS) AF: 0.677 AC: 3498 AN: 5168

South Asian (SAS) AF: 0.496 AC: 2394 AN: 4828

European-Finnish (FIN) AF: 0.787 AC: 8342 AN: 10594

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47755 AN: 67962

Other (OTH) AF: 0.614 AC: 1293 AN: 2106

Alfa AF: 0.654 Hom.: 4274

Bravo AF: 0.610

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.55
PhyloP100		-0.28

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: rs9297781;

hg19: chr8-130029366;