ENST00000630386.2:n.100+11903C>T

Variant names:

• chr8-128952627-G-A
• rs17242358
• ENST00000630386.2:n.100+11903C>T

Variant summary

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

The ENST00000630386.2(CCDC26):​n.100+11903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,120 control chromosomes in the GnomAD database, including 1,701 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 0.14 (1701 hom., cov: 32)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000630386.2	n.100+11903C>T		intron_variant	Intron 2 of 6	5
CCDC26	ENST00000643616.1	n.136+11903C>T		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-47459C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20608 AN: 152002 Hom.: 1701 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.135 AC: 20602 AN: 152120 Hom.: 1701 Cov.: 32 AF XY: 0.131 AC XY: 9722 AN XY: 74362

African (AFR) AF: 0.0645 AC: 2677 AN: 41518

American (AMR) AF: 0.125 AC: 1905 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3472

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5172

South Asian (SAS) AF: 0.0724 AC: 349 AN: 4818

European-Finnish (FIN) AF: 0.120 AC: 1271 AN: 10586

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13195 AN: 67974

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.172 Hom.: 7205

Bravo AF: 0.134

Asia WGS AF: 0.0400 AC: 141 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	0.99
DANN	Benign	0.53
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17242358; hg19: chr8-129964873;