ENST00000446592.7:n.312+50253T>C

Variant names:

• chr8-129629675-A-G
• rs6470745
• ENST00000446592.7:n.312+50253T>C

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+50253T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,156 control chromosomes in the GnomAD database, including 2,622 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 0.18 (2622 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	NR_130917.1		n.312+50253T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.312+50253T>C		intron	N/A
	CCDC26	ENST00000642958.2		n.474-1585T>C		intron	N/A
	CCDC26	ENST00000645432.1		n.364-42653T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27021 AN: 152038 Hom.: 2609 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.178 AC: 27052 AN: 152156 Hom.: 2622 Cov.: 32 AF XY: 0.181 AC XY: 13499 AN XY: 74398

African (AFR) AF: 0.102 AC: 4255 AN: 41530

American (AMR) AF: 0.228 AC: 3477 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3472

East Asian (EAS) AF: 0.300 AC: 1546 AN: 5156

South Asian (SAS) AF: 0.192 AC: 922 AN: 4814

European-Finnish (FIN) AF: 0.223 AC: 2363 AN: 10588

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13258 AN: 68000

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.187 Hom.: 8812

Bravo AF: 0.179

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs6470745; hg19: chr8-130641921;