chr8-128938598-C-T

Position:

• chr8-128938598-C-T

Variant summary

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

The ENST00000675388.1(CCDC26):​n.654-121904G>A 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 0.32 in 151,730 control chromosomes in the GnomAD database, including 8,348 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 0.32 (8348 hom., cov: 31)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000675388.1	n.654-121904G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48539 AN: 151612 Hom.: 8348 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.320 AC: 48564 AN: 151730 Hom.: 8348 Cov.: 31 AF XY: 0.314 AC XY: 23273 AN XY: 74124

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0440

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.337

Alfa AF: 0.377 Hom.: 20041

Bravo AF: 0.316

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7017252; hg19: chr8-129950844;