rs1372449

Positions:

• chr8-128938144-G-A
• chr8-128938144-G-C

Variant summary

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

The ENST00000675388.1(CCDC26):​n.654-121450C>T 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 0.316 in 151,904 control chromosomes in the GnomAD database, including 8,141 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 (8141 hom., cov: 32)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 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.654-121450C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48049 AN: 151786 Hom.: 8141 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.316 AC: 48074 AN: 151904 Hom.: 8141 Cov.: 32 AF XY: 0.311 AC XY: 23065 AN XY: 74230

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.0439

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.333

Alfa AF: 0.226 Hom.: 516

Bravo AF: 0.313

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372449; hg19: chr8-129950390;