8-129652161-T-C

Variant names:

• chr8-129652161-T-C
• rs9656979
• ENST00000446592.7:n.312+27767A>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+27767A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,874 control chromosomes in the GnomAD database, including 11,410 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 0.38 (11410 hom., cov: 30)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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.312+27767A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.312+27767A>G		intron	N/A
	CCDC26	ENST00000642958.2		n.473+16038A>G		intron	N/A
	CCDC26	ENST00000645432.1		n.363+27767A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57116 AN: 151756 Hom.: 11403 Cov.: 30

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.376 AC: 57144 AN: 151874 Hom.: 11410 Cov.: 30 AF XY: 0.383 AC XY: 28453 AN XY: 74212

African (AFR) AF: 0.224 AC: 9291 AN: 41422

American (AMR) AF: 0.424 AC: 6477 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3466

East Asian (EAS) AF: 0.534 AC: 2743 AN: 5136

South Asian (SAS) AF: 0.461 AC: 2216 AN: 4808

European-Finnish (FIN) AF: 0.451 AC: 4755 AN: 10548

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28566 AN: 67926

Other (OTH) AF: 0.388 AC: 816 AN: 2102

Alfa AF: 0.408 Hom.: 15016

Bravo AF: 0.371

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9656979; hg19: chr8-130664407;