rs987525

Variant names:

• chr8-128933908-C-A
• rs987525
• ENST00000630386.2:n.101-13025G>T

Variant summary

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

The ENST00000643616.1(CCDC26):​n.136+30622G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,970 control chromosomes in the GnomAD database, including 9,264 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 0.30 (9264 hom., cov: 31)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 91 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 = 0.565 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	ENST00000630386.2	TSL:5	n.101-13025G>T		intron	N/A
	CCDC26	ENST00000643616.1		n.136+30622G>T		intron	N/A
	CCDC26	ENST00000644557.1		n.411-28740G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46137 AN: 151852 Hom.: 9237 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.304 AC: 46208 AN: 151970 Hom.: 9264 Cov.: 31 AF XY: 0.296 AC XY: 21998 AN XY: 74262

African (AFR) AF: 0.571 AC: 23634 AN: 41406

American (AMR) AF: 0.228 AC: 3484 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3468

East Asian (EAS) AF: 0.0665 AC: 345 AN: 5186

South Asian (SAS) AF: 0.178 AC: 858 AN: 4816

European-Finnish (FIN) AF: 0.129 AC: 1362 AN: 10558

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14860 AN: 67956

Other (OTH) AF: 0.283 AC: 595 AN: 2104

Alfa AF: 0.240 Hom.: 24498

Bravo AF: 0.324

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.38

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: rs987525;

hg19: chr8-129946154;