rs1519847

chr8-128903514-C-T

Variant summary

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

The ENST00000675388.1(CCDC26):n.654-86820G>A 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 0.45 in 151,982 control chromosomes in the GnomAD database, including 17,267 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 0.45 (17267 hom., cov: 32)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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.654-86820G>A		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000643616.1	n.136+61016G>A		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676248.1	n.101-88976G>A		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676407.1	n.493-75420G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68329 AN: 151864 Hom.: 17240 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.450 AC: 68404 AN: 151982 Hom.: 17267 Cov.: 32 AF XY: 0.442 AC XY: 32821 AN XY: 74292

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.432

Alfa AF: 0.414 Hom.: 2812

Bravo AF: 0.463

Asia WGS AF: 0.303 AC: 1053 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519847; hg19: chr8-129915760;