rs997310

Variant names:

• chr8-128908034-C-A
• rs997310
• ENST00000630386.2:n.506-2901G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-128908034-C-A
• chr8-128908034-C-G
• chr8-128908034-C-T

Variant summary

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

The ENST00000630386.2(CCDC26):​n.506-2901G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,712 control chromosomes in the GnomAD database, including 8,975 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 0.32 (8975 hom., cov: 32)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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	ENST00000630386.2	n.506-2901G>T		intron_variant	Intron 6 of 6	5
CCDC26	ENST00000643616.1	n.136+56496G>T		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-2866G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49108 AN: 151596 Hom.: 8956 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.324 AC: 49162 AN: 151712 Hom.: 8975 Cov.: 32 AF XY: 0.318 AC XY: 23580 AN XY: 74150

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0697

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.321

Alfa AF: 0.279 Hom.: 3967

Bravo AF: 0.340

Asia WGS AF: 0.183 AC: 634 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.036
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997310; hg19: chr8-129920280;