rs9297781

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000644194.1	n.822+719T>G		intron_variant	Intron 6 of 6
CCDC26	ENST00000644557.1	n.410+85170T>G		intron_variant	Intron 3 of 3
CCDC26	ENST00000674766.1	n.451+719T>G		intron_variant	Intron 5 of 5

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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.614

Alfa AF: 0.662 Hom.: 4193

Bravo AF: 0.610

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9297781; hg19: chr8-130029366;