ENST00000446592.7:n.361-35001A>C

Variant names:

• chr8-129405378-T-G
• rs2568409
• ENST00000446592.7:n.361-35001A>C

Variant summary

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

The ENST00000446592.7(CCDC26):​n.361-35001A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,222 control chromosomes in the GnomAD database, including 2,494 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 0.17 (2494 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.361-35001A>C		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.138-35001A>C		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.138-5694A>C		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.138-5694A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.361-35001A>C		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.136-35001A>C		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.111-5694A>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26306 AN: 152104 Hom.: 2491 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.173 AC: 26305 AN: 152222 Hom.: 2494 Cov.: 32 AF XY: 0.168 AC XY: 12519 AN XY: 74420

African (AFR) AF: 0.211 AC: 8752 AN: 41528

American (AMR) AF: 0.151 AC: 2307 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1441 AN: 5166

South Asian (SAS) AF: 0.154 AC: 745 AN: 4826

European-Finnish (FIN) AF: 0.0984 AC: 1044 AN: 10612

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10852 AN: 68002

Other (OTH) AF: 0.189 AC: 400 AN: 2116

Alfa AF: 0.140 Hom.: 604

Bravo AF: 0.179

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs2568409; hg19: chr8-130417624;