rs2116457

Variant names:

• chr8-128795555-A-G
• rs2116457
• ENST00000643616.1:n.232+12519T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-128795555-A-G
• chr8-128795555-A-T

Variant summary

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

The ENST00000643616.1(CCDC26):​n.232+12519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,066 control chromosomes in the GnomAD database, including 16,623 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 0.46 (16623 hom., cov: 32)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

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 (EAS) allele frequency at 95% confidence interval = 0.802 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	ENST00000643616.1	n.232+12519T>C		intron_variant	Intron 3 of 3
CCDC26	ENST00000675388.1	n.797+12519T>C		intron_variant	Intron 8 of 8
CCDC26	ENST00000676248.1	n.325+12519T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69314 AN: 151948 Hom.: 16587 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.456 AC: 69414 AN: 152066 Hom.: 16623 Cov.: 32 AF XY: 0.464 AC XY: 34492 AN XY: 74322

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.444

Alfa AF: 0.424 Hom.: 4819

Bravo AF: 0.472

Asia WGS AF: 0.646 AC: 2246 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	5.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116457; hg19: chr8-129807801;