rs17241253

chr8-128877942-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000675388.1(CCDC26):n.654-61248A>G variant causes a intron, non coding transcript 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 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.654-61248A>G		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000643616.1	n.137-69773A>G		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676248.1	n.101-63404A>G		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676407.1	n.493-49848A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0536

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0707

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.123

Alfa AF: 0.171 Hom.: 775

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17241253; hg19: chr8-129890188;