chr8-128852347-C-T

Variant names:

• chr8-128852347-C-T
• rs17818958
• ENST00000643616.1:n.137-44178G>A

Variant summary

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

The ENST00000643616.1(CCDC26):​n.137-44178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,924 control chromosomes in the GnomAD database, including 10,786 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 0.37 (10786 hom., cov: 31)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 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.137-44178G>A		intron_variant	Intron 2 of 3
CCDC26	ENST00000675388.1	n.654-35653G>A		intron_variant	Intron 6 of 8
CCDC26	ENST00000676248.1	n.101-37809G>A		intron_variant	Intron 1 of 4
CCDC26	ENST00000676407.1	n.493-24253G>A		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55632 AN: 151806 Hom.: 10781 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.366 AC: 55643 AN: 151924 Hom.: 10786 Cov.: 31 AF XY: 0.360 AC XY: 26689 AN XY: 74234

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.378

Alfa AF: 0.279 Hom.: 710

Bravo AF: 0.360

Asia WGS AF: 0.303 AC: 1056 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	0.80
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17818958; hg19: chr8-129864593;