rs2116457

chr8-128795555-A-Gchr8-128795555-A-T

Variant summary

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

The ENST00000675388.1(CCDC26):n.797+12519T>C 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 0.456 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 ENST00000675388.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.797+12519T>C		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000643616.1	n.232+12519T>C		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676248.1	n.325+12519T>C		intron_variant, non_coding_transcript_variant

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;