rs10464870

Positions:

• chr8-129465577-C-T

Variant summary

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

The NR_130917.1(CCDC26):​n.360+15066G>A 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 0.805 in 152,144 control chromosomes in the GnomAD database, including 49,698 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 0.81 (49698 hom., cov: 32)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+15066G>A		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.138-95200G>A		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.138-65893G>A		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.138-65893G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000675388.1	n.182+15066G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122466 AN: 152028 Hom.: 49669 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.805 AC: 122545 AN: 152144 Hom.: 49698 Cov.: 32 AF XY: 0.801 AC XY: 59552 AN XY: 74376

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.817

Alfa AF: 0.797 Hom.: 95787

Bravo AF: 0.819

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10464870; hg19: chr8-130477823;