8-129447166-T-C

Variant names:

• chr8-129447166-T-C
• rs1368136
• ENST00000446592.7:n.360+33477A>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.360+33477A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,752 control chromosomes in the GnomAD database, including 16,201 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 0.46 (16201 hom., cov: 31)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

ENSG00000253926 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+33477A>G		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.138-76789A>G		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.138-47482A>G		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.138-47482A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.360+33477A>G		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.136-76789A>G		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.111-47482A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69130 AN: 151634 Hom.: 16199 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.456 AC: 69144 AN: 151752 Hom.: 16201 Cov.: 31 AF XY: 0.457 AC XY: 33863 AN XY: 74166

African (AFR) AF: 0.393 AC: 16256 AN: 41336

American (AMR) AF: 0.583 AC: 8901 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 1999 AN: 3466

East Asian (EAS) AF: 0.678 AC: 3488 AN: 5144

South Asian (SAS) AF: 0.418 AC: 2006 AN: 4802

European-Finnish (FIN) AF: 0.364 AC: 3824 AN: 10514

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31035 AN: 67920

Other (OTH) AF: 0.485 AC: 1021 AN: 2106

Alfa AF: 0.460 Hom.: 8088

Bravo AF: 0.471

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.46
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1368136; hg19: chr8-130459412;