rs17241253

Variant names:

• chr8-128877942-T-C
• rs17241253
• ENST00000643616.1:n.137-69773A>G

Variant summary

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

The ENST00000643616.1(CCDC26):​n.137-69773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,178 control chromosomes in the GnomAD database, including 1,501 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 0.13 (1501 hom., cov: 32)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 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	ENST00000643616.1	n.137-69773A>G		intron_variant	Intron 2 of 3
CCDC26	ENST00000675388.1	n.654-61248A>G		intron_variant	Intron 6 of 8
CCDC26	ENST00000676248.1	n.101-63404A>G		intron_variant	Intron 1 of 4
CCDC26	ENST00000676407.1	n.493-49848A>G		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19118 AN: 152060 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.0536

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.126 AC: 19111 AN: 152178 Hom.: 1501 Cov.: 32 AF XY: 0.122 AC XY: 9039 AN XY: 74384

African (AFR) AF: 0.0536 AC: 2224 AN: 41524

American (AMR) AF: 0.114 AC: 1736 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0707 AC: 341 AN: 4826

European-Finnish (FIN) AF: 0.109 AC: 1149 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12643 AN: 68002

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.169 Hom.: 777

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.025
DANN	Benign	0.66
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17241253; hg19: chr8-129890188;