rs759944

chr8-128775180-A-Gchr8-128775180-A-T

Variant summary

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

The ENST00000675388.1(CCDC26):n.797+32894T>C 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 0.486 in 151,954 control chromosomes in the GnomAD database, including 18,620 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 0.49 (18620 hom., cov: 31)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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.797+32894T>C		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000643616.1	n.232+32894T>C		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676248.1	n.325+32894T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73815 AN: 151836 Hom.: 18606 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.486 AC: 73881 AN: 151954 Hom.: 18620 Cov.: 31 AF XY: 0.479 AC XY: 35548 AN XY: 74272

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.478

Alfa AF: 0.474 Hom.: 2361

Bravo AF: 0.496

Asia WGS AF: 0.412 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759944; hg19: chr8-129787426;