8-129559864-G-C

Variant names:

• chr8-129559864-G-C
• rs10956483
• ENST00000446592.7:n.313-79174C>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.313-79174C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,144 control chromosomes in the GnomAD database, including 2,796 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 0.16 (2796 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 12 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446592.7. 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
	CCDC26	NR_130917.1		n.313-79174C>G		intron	N/A
	CCDC26	NR_130918.1		n.137+15018C>G		intron	N/A
	CCDC26	NR_130919.1		n.137+15018C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.313-79174C>G		intron	N/A
	CCDC26	ENST00000523151.6	TSL:1	n.135+15018C>G		intron	N/A
	CCDC26	ENST00000520048.1	TSL:3	n.110+15018C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24793 AN: 152028 Hom.: 2785 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.163 AC: 24805 AN: 152144 Hom.: 2796 Cov.: 32 AF XY: 0.169 AC XY: 12577 AN XY: 74368

African (AFR) AF: 0.0571 AC: 2372 AN: 41524

American (AMR) AF: 0.277 AC: 4227 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3472

East Asian (EAS) AF: 0.546 AC: 2817 AN: 5162

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1708 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11470 AN: 67986

Other (OTH) AF: 0.178 AC: 375 AN: 2110

Alfa AF: 0.160 Hom.: 1335

Bravo AF: 0.169

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		0.077

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: rs10956483;

hg19: chr8-130572110;