rs9297781

Positions:

• chr8-129017120-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000675388.1(CCDC26):​n.653+85170T>G variant causes a intron, non coding transcript 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 ENST00000675388.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.653+85170T>G		intron_variant, non_coding_transcript_variant

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;