rs10098310

Variant names:

• chr8-129601368-G-A
• rs10098310
• ENST00000446592.7:n.312+78560C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+78560C>T variant causes a intron 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 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 11 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446592.7. 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
	CCDC26	NR_130917.1		n.312+78560C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.312+78560C>T		intron	N/A
	CCDC26	ENST00000645432.1		n.364-14346C>T		intron	N/A
	CCDC26	ENST00000663066.2		n.634-14346C>T		intron	N/A

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

African (AFR) AF: 0.471 AC: 19506 AN: 41388

American (AMR) AF: 0.549 AC: 8382 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2115 AN: 5164

South Asian (SAS) AF: 0.662 AC: 3182 AN: 4808

European-Finnish (FIN) AF: 0.592 AC: 6236 AN: 10534

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38931 AN: 67930

Other (OTH) AF: 0.550 AC: 1157 AN: 2104

Alfa AF: 0.548 Hom.: 35822

Bravo AF: 0.529

Asia WGS AF: 0.537 AC: 1862 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.86

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: rs10098310;

hg19: chr8-130613614;