rs1155582

Variant names:

• chr8-128882775-C-G
• rs1155582
• ENST00000643616.1:n.137-74606G>C

Variant summary

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

The ENST00000643616.1(CCDC26):​n.137-74606G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,040 control chromosomes in the GnomAD database, including 31,801 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 0.64 (31801 hom., cov: 33)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 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.137-74606G>C		intron	N/A
	CCDC26	ENST00000675388.1		n.654-66081G>C		intron	N/A
	CCDC26	ENST00000676248.1		n.101-68237G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97520 AN: 151922 Hom.: 31768 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.642 AC: 97605 AN: 152040 Hom.: 31801 Cov.: 33 AF XY: 0.643 AC XY: 47766 AN XY: 74314

African (AFR) AF: 0.601 AC: 24903 AN: 41462

American (AMR) AF: 0.717 AC: 10964 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4869 AN: 5168

South Asian (SAS) AF: 0.643 AC: 3099 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 5995 AN: 10542

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43776 AN: 67968

Other (OTH) AF: 0.628 AC: 1329 AN: 2116

Alfa AF: 0.636 Hom.: 3868

Bravo AF: 0.655

Asia WGS AF: 0.762 AC: 2652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		0.097

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: rs1155582;

hg19: chr8-129895021;