rs10098310

Positions:

• chr8-129601368-G-A
• chr8-129601368-G-T

Variant summary

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

The NR_130917.1(CCDC26):​n.312+78560C>T 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 0.54 in 151,858 control chromosomes in the GnomAD database, including 22,463 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 0.54 (22463 hom., cov: 31)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.312+78560C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+78560C>T		intron_variant, non_coding_transcript_variant		1
CCDC26	ENST00000645432.1	n.364-14346C>T		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000663066.1	n.170-14346C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81904 AN: 151740 Hom.: 22447 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.540 AC: 81950 AN: 151858 Hom.: 22463 Cov.: 31 AF XY: 0.542 AC XY: 40272 AN XY: 74254

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.550

Alfa AF: 0.446 Hom.: 1370

Bravo AF: 0.529

Asia WGS AF: 0.537 AC: 1862 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10098310; hg19: chr8-130613614;