rs1519847

Variant names:

• chr8-128903514-C-T
• rs1519847
• ENST00000643616.1:n.136+61016G>A

Variant summary

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

The ENST00000643616.1(CCDC26):​n.136+61016G>A variant causes a intron 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 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643616.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000643616.1		n.136+61016G>A		intron	N/A
	CCDC26	ENST00000675388.1		n.654-86820G>A		intron	N/A
	CCDC26	ENST00000676248.1		n.101-88976G>A		intron	N/A

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

African (AFR) AF: 0.677 AC: 28047 AN: 41430

American (AMR) AF: 0.341 AC: 5207 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3472

East Asian (EAS) AF: 0.104 AC: 537 AN: 5178

South Asian (SAS) AF: 0.376 AC: 1813 AN: 4820

European-Finnish (FIN) AF: 0.289 AC: 3053 AN: 10548

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26895 AN: 67956

Other (OTH) AF: 0.432 AC: 910 AN: 2106

Alfa AF: 0.416 Hom.: 3625

Bravo AF: 0.463

Asia WGS AF: 0.303 AC: 1053 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.075

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: rs1519847;

hg19: chr8-129915760;