rs17241908

Variant names:

• chr8-128932630-C-G
• rs17241908
• ENST00000630386.2:n.101-11747G>C

Variant summary

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

The ENST00000630386.2(CCDC26):​n.101-11747G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,186 control chromosomes in the GnomAD database, including 2,231 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 0.16 (2231 hom., cov: 31)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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.101-11747G>C		intron_variant	Intron 2 of 6	5
CCDC26	ENST00000643616.1	n.136+31900G>C		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-27462G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24624 AN: 152068 Hom.: 2231 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.162 AC: 24627 AN: 152186 Hom.: 2231 Cov.: 31 AF XY: 0.157 AC XY: 11687 AN XY: 74398

African (AFR) AF: 0.129 AC: 5354 AN: 41520

American (AMR) AF: 0.137 AC: 2094 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5182

South Asian (SAS) AF: 0.0915 AC: 441 AN: 4818

European-Finnish (FIN) AF: 0.126 AC: 1337 AN: 10594

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14184 AN: 68004

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.180 Hom.: 346

Bravo AF: 0.161

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs17241908; hg19: chr8-129944876;